Binding Studies Research Articles

Abstract 3122: Preclinical development of a novel camptothecin-based antibody-drug conjugate targeting solid tumors expressing Claudin-6

Abstract Claudin-6 is a member of the claudin family and consists of four transmembrane helices, two extracellular loops, and an amino- and carboxyl-terminal tail with a PDZ-binding motif in the cytoplasm. It is involved in the formation of tight junctions and is expressed in developing human epithelial structures during early-to-mid gestation while expression in iadult tissues is mostly absent. Claudin-6 expression is upregulated in ovarian cancer, testicular cancer, endometrial cancer, non-small cell lung cancer (NSCLC) and gastric cancer. Here, the generation and preclinical characterization of a novel Claudin-6 specific antibody-drug conjugate (ADC) is described, composed of a humanized IgG1 directed against human Claudin-6 site-specifically conjugated a novel payload containing a valine-alanine cleavable linker and a camptothecin warhead with a drug to antibody ratio of 6. FcγR-mediated effector function of the ADC was abrogated via mutations in the Fc portion of the antibody. The purpose of this study was to evaluate the expression of Claudin-6 in different tumour indications and characterise the in vitro and in vivo anti-tumour activity in human cancer cell lines and patient-derived xenograft (PDX) models. In addition, the tolerability of the ADC was evaluated in a repeat-dose toxicity study cynomolgus monkeys. Cell binding studies using Fabs showed high affinity binding to Claudin-6, while affinity for Claudin-9 was 16-fold lower with no binding to Claudin-3 and Claudin-4. Cross-reactivity with cynomolgus monkey and mouse Claudin-6 was also demonstrated. Fcgamma receptor binding studies confirmed the strongly reduced binding of the antibody to FcγI, FcγI,IIa, FcγIIb and FcγIIa, consistent with the introduction of mutations in the Fc domain of the antibody. In vitro, the Claudin-6 ADC showed potent and specific cytotoxicity against various Claudin-6-expressing solid cancer cell lines, including OVCAR3, PA-1, OV-90, FU-97, BeWo, NTERA-2 and NUGC3 in comparison to a non-binding control ADC conjugated to the same payload, and it also showed potent bystander killing. In vivo, a single dose intravenous (IV) of the Claudin-6 ADC demonstrated potent anti-tumour activity in multiple solid tumour xenograft models, including OVCAR3 and PA-1. Furthermore, administration of the Claudin-6 ADC to cynomolgus monkeys was well tolerated up to 40 mg/kg IV when given on Day 1 and 22. Cell membrane expression of Claudin-6 was confirmed by immunohistochemistry (IHC) in ovarian cancer (70%), testicular cancer (98%), endometrial cancer (30%), NSCLC (28%) and gastric cancer (24%), confirming expression of Claudin-6 in indications with high unmet need. In summary, this novel Claudin-6 ADC demonstrated potent, specific anti-tumour activity in Claudin-6 expressing cancer-derived models and was well tolerated in cynomolgus monkey, supporting future clinical development of this ADC. Citation Format: Nicola Tsang, Nicolas Veillard, Elizabeth Horsley, Karin Havenith, Narinder Janghra, Kristina Zaitseva, Cecile Oblette, Ian Kirby, Paul W. Hogg, Francesca Zammarchi, Lolke de Haan, Patrick H. van Berkel. Preclinical development of a novel camptothecin-based antibody-drug conjugate targeting solid tumors expressing Claudin-6 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3122.

Abstract 2345: Docking and molecular dynamic simulations of mithramycin against Sp1, Sp3, and survivin

Abstract Purpose: Therapeutic targeting of transcription factors, Specificity protein (Sp)1 and Sp3 and their downstream effectors, such as survivin, are studied in various cancers. Due to role in in poorer cancer prognoses in several cancers their downregulation has been investigated as an effective treatment approach. Mithramycin (Mit) showed innate anti-cancer properties by targeting Sp proteins through GC/GT DNA binding interference. Recent studies have given new insights into further mechanisms of action of Mit, however in-depth binding and mechanistic studies are lacking. Our objective is to investigate Mit’s specific binding interactions with Sp1, Sp3, and survivin. Methods: Protein structures and sequences for Sp1, Sp3, and survivin (ID: P08047, Q02447, and O153392, respectively) were retrieved from UniProtKB database. Experimental predicted structures for Sp1 and Sp3 were obtained from AlphaFold. Sequence lengths of Sp1 and Sp3 were 785 and 781 amino acids (aa), domain regions of Sp1 (619-785) and Sp3 (461-781) were note. Survivin structure was obtained from PDB and was comprised of 142 aa. Co-crystallized compounds were removed during analyses using BIOVIA Discovery Studio 4.5 Visualizer. Prediction of binding sites and docking were performed using CASTp, GHECOM, DEPTH tools, glide, and AutoDock 4.2 software. Energy minimization and Molecular dynamics simulations were performed in the Schrödinger suite. Results: Binding sites were identified for Sp1, Sp3, and survivin. Simulated docking demonstrated multiple binding complexes and varying binding energies. The most efficient binding was seen with Sp1 and Sp3. RMSF and RMSD simulations revealed stabilization of Sp1-, Sp3-, and survivin-Mit complexes. This shows Mithramycin can potentially inhibit all three proteins, with slightly more stability with Sp1 and Sp3. Radius of gyration (rGyr), H-bond analysis, and solvent accessible surface area (SASA) support docking findings with Mit-protein complexes remaining stable in the binding pocket, forming new H-bonds, and altering hydrophilic and hydrophobic interaction areas. Conclusion: Our findings warrant further in vitro testing of the ability of Mit to interact with a wider range of oncogenic targets. While we only tested the ability of Mit to interact with Sp1, Sp3 and survivin, similar model can be used to evaluate the interaction with other critical proteins associated with cancer and to further elucidate mechanisms of action. These finding are crucial to understanding base mechanistic abilities and can be useful to test additional agents for their ability to interact with Sp1 or survivin. Citation Format: Christoffer Briggs Lambring, Santosh K. Behera, Riyaz Basha. Docking and molecular dynamic simulations of mithramycin against Sp1, Sp3, and survivin [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2345.

Abstract 1327: Affinity tuning anti-CD123 chimeric antigen receptor natural killer cell therapy to treat acute myeloid leukemia

Abstract Acute myeloid leukemia (AML) is a highly prevalent blood and bone marrow cancer characterized by the uncontrolled growth of abnormal myeloblasts. Current treatments for AML often result in systemic toxicities for patients, many of whom will still experience relapse. There is thus an unmet need to develop safer and more effective therapies targeting AML. Chimeric antigen receptor (CAR) T cells, which are engineered to express a cancer-targeting extracellular antibody single-chain variable fragment (scFv) linked to an intracellular T cell-activating domain, have shown promise in treating B cell leukemias, but their success has been limited in myeloid leukemias. This is due in part to the lack of AML-specific target antigens. Moreover, impaired T cell function, a hallmark of AML, is also problematic when relying on autologous T cell activation upon reinfusion. We overcame the limitations of CAR T therapy in AML by developing CAR-expressing natural killer (NK) cells targeting CD123. While present on both healthy and AML cells, CD123 is expressed at >10-fold higher levels on malignant cells. Furthermore, use of NK allows use of fully functional allogeneic cells from healthy donors, since NK cells do not induce graft-versus-host-disease. To optimize the tumor cell selectivity of CAR NK cells, we employed the yeast display directed evolution platform to isolate anti-CD123 scFvs with varying affinities and are identifying and characterizing clones that maximize the interaction with CD123high AML cells over healthy CD123low cells, as determined by binding, cytotoxicity, cytokine secretion, and intracellular signaling studies. Collectively, our efforts introduce a new paradigm for engineered cell therapeutics with significant promise for AML treatment. Citation Format: Monika Kizerwetter, Huilin Yang, Ruyan Rahnama, Challice Bonifant, Jamie Spangler. Affinity tuning anti-CD123 chimeric antigen receptor natural killer cell therapy to treat acute myeloid leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1327.

Abstract 5778: Determining the structure and function relationship of the oxysterol-binding protein (OSBP) to guide drug development

Abstract The human Oxysterol Binding Protein Structure and function relationship remains elusive, yet the anti-cancer and antiviral molecules library targeting OSBP and OSBP-Related proteins (ORPs) continues to grow. OSBP is a ubiquitously expressed protein in most eukaryotes, functioning as a master lipid sensor and cholesterol regulator in cells. OSBP and its closely related protein ORP4 are also reported to be essential in several human diseases, including viral infection and cancer cell proliferation. Our lab has shown that the natural product OSW-1 has potential anti-viral and anti-cancer activity through targeting OSBP and ORP4, as confirmed with protein-ligand interactions that showed binding with high affinity. Moreover, several anti-cancer molecules targeting the ORPs provoke different protein conformation changes and, therefore, lead to varying OSBP functions. However, the structure of full-length OSBP is still unknown, which leaves a gap in knowledge regarding the compounds’ mechanism of action or how OSBP could be established as a molecular anti-cancer target. Our goal is to determine the structure and function relationship of OSBP with emphasis on the effect of small molecule ligands on cellular OSBP levels and function. In pursuit of this research goal, we aim to determine the in vitro activity of OSW-1 analogs (OA) isolated in our lab, as well as determine their interaction with OSBP and ORP4 proteins in multiple cancer cell lines. We mainly seek to determine the structure and ligand interaction with the OSBP-ligand binding domain (LBD) and full-length OSBP to shed light on the conformation changes that occur upon ligand binding. Preliminary data indicate that the tested OA compounds are active in multiple cancer cell lines with reduced OSBP levels effect, suggesting a similar mechanism of action to OSW-1. A transient expression of full-length OSBP and LBD showed that the truncated OSBP (LBD) was mostly found in the pellet, which could imply low solubility, while the full-length OSBP showed sufficient solubility. Our efforts are currently focused on purifying full-length OSBP. We are also working towards purifying full-length OSBP with a cleavage site that allows cutting out the LBD, thus solving the insolubility issue. Once obtained, the full-length OSBP and the ligand binding domain will be used for both binding and structure determination studies. Citation Format: Ruth Fiona Bayimenye, Jorge L. Berrios-Rivera, Susan Nimmo, Christina R. Bourne, Anthony W. Burgett. Determining the structure and function relationship of the oxysterol-binding protein (OSBP) to guide drug development [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5778.

Abstract 3200: Assessing the utility of cell membrane lipid-extracted nanoliposomes (CLENs) as a targeted drug delivery system for pancreatic cancer

Abstract Background: Pancreatic cancer is a challenging type of cancer to treat as evidenced by a 9% 5-year survival and a dismal rate of mortality. Nanoparticles represent a revolutionary treatment method, primarily due to characteristics including cellular absorption, boosting therapeutic effectiveness, and mitigating side effects through localized actions. For nanomedicine, optimizing liposome formulations is crucial for achieving the highest level of specificity in drug targeting. This study aims to evaluate cellular interaction of pancreatic cancer lipid-extract modified nanoliposomes when compared to unmodified varieties in vitro. Method: Cell membrane lipid-extracted nanoliposomes (CLENs) were prepared via the thin film evaporation technique. The composition included various compositions and ratios of DOPC, DOTAP, Cholesterol, DPPE-PEG-5000, and lipid extracts derived from MS1-VEGF target cells. MS1-VEGF was the cellular model of pancreatic cancer used for this study. Cellular binding studies were performed using cellular suspension and adherent cell populations. Studies were performed in 48-well plates under different experimental conditions including alterations in time of incubation, and periods of cellular exposure to dual humidified and oscillation environments in the presence of lipid-extracted (LE) nanoliposomal preparations and conventional controls. Results: The particle size for nanoliposomes employed for this study was approximately 115 ± 0.7 nm for control and 128 ± 2.7 nm for experimental (lipid extract-modified) nanoliposomes. Following cellular exposure to different lipid extract concentrations (typically 0 to 100 nmoles per ml of growth medium), the fluorescence values demonstrated increased cellular uptake with greater LE content for floating and adhered MS1-VEGF cell populations. With the floating cells, LE-modified nanoliposomes demonstrated significantly higher fluorescence intensity values compared to conventional nanoliposomes. Similarly, with MS1-VEGF adherent cells, LE-modified nanoliposomes targeted cells to a greater extent compared to unmodified controls. Conclusions: The increased cellular uptake of CLENs designed for targeting pancreatic tumor cells (both floating and adherent cells) demonstrated an improvement over the use of conventional nanoliposomes under similar experimental conditions. Further research is needed to fully explore the potential use of CLENs for targeting and treatment of pancreatic cancer. Citation Format: Khaznah Alshammari, Sergio Verdery, Sujin George, Robert B Campbell. Assessing the utility of cell membrane lipid-extracted nanoliposomes (CLENs) as a targeted drug delivery system for pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3200.

Abstract 4484: Discovery of a potential first-in-class Za targeted small molecule inhibitor of ADAR1 p150 which demonstrates strong anti-tumor efficacy

Abstract Background: Adenosine deaminase, RNA specific (ADAR1), catalyzes the hydrolytic deamination of adenosine (A) to inosine (I) in double-stranded (ds) RNAs. ADAR1 has two isoforms: p110 in the nucleus and p150 in the cytoplasm. Both isoforms alter the coding and non-coding sections of self-dsRNA. The ADAR1 p150 isoform is expressed from an interferon (IFN)-response promoter and has a Z-DNA/Z-RNA binding domain at the N-terminus. ADAR1 has been implicated in promoting cell survival and resistance to immune response in several cancer types like multiple myeloma, breast, lung, liver, and skin cancer. Inhibition of ADAR1 p150 has the potential to enhance anti-tumor efficacy as monotherapy and in combination with other therapeutic modalities. The Zα domain of ADAR1 p150 provides exclusivity to p150 compared to the other isoforms. Herein, we outline the discovery of a potential first-in-class Zα targeted ADAR1 p150 inhibitor and degrader for cancer immunotherapy. Methods: AVA-ADR-001 was identified through a high throughput p110 knockout cell-based assay. The ability of AVA-ADR-001 to induce interferons was confirmed in various cell lines. The anti-tumor efficacy of AVA-ADR-001 was evaluated in B16F10 syngeneic melanoma mice model as monotherapy and in combination with anti-PD-1. PROTAC AVA-ADR-703 was used to demonstrate selective degradation of the ADAR1 p150 protein. Results: We have discovered AVA-ADR-001, a novel small molecule inhibitor of ADAR1 which significantly increases the IFN response in vitro in an MDA5-dependent manner. In vitro binding studies confirm that AVA-ADR-001 binds to the Zα domain of ADAR1 with low nM potency. AVA-ADR-001 demonstrates anti-tumor efficacy 1.5X superior to anti-PD1 ICB non-responsive tumor models. In addition, the AVA-ADR-001 monotherapy and combination groups showed a significant upregulation of numerous interferon-stimulated genes, including IFIH1, IFN-β, and CXCL-10. Finally, targeted protein degradation of ADAR1 p150 while sparing ADAR1 p110 was confirmed when cells were treated with AVA-ADR-703 with nM DC50, the PROTAC variant of AVA-ADR-001. Conclusions: To our knowledge, AVA-ADR-001 and AVA-ADR-703 are the first selective Zα-targeted small molecule inhibitor and degrader of ADAR1 p150 respectively to be disclosed. As a powerful and targeted first-in-class ADAR1 inhibitor, AVA-ADR-001 has demonstrated a strong induction of interferon (IFN) in a number of cancer cell lines and in vivo. AVA-ADR-001 has also demonstrated strong in vivo anti-tumor efficacy as monotherapy and in combination with anti-PD1. Furthermore, AVA-ADR-703 demonstrates selective and highly efficient degradation of ADAR1 p150 while sparing ADAR1 p110. Given that ADAR1 has a pro-metastatic and immune-suppressive role, AVA-ADR-001 and AVA-ADR-703 have significant potential to emerge as strong cancer immunotherapy candidates. Citation Format: Avijit Goswami, Sandeep Goyal, Kawaljit Singh, Princy Khurana, Barnali Deb, Aditya Kulkarni. Discovery of a potential first-in-class Za targeted small molecule inhibitor of ADAR1 p150 which demonstrates strong anti-tumor efficacy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4484.

Synthesis and Macrodomain Binding of Gln-carba-ADPr-peptide.

Mono-ADP-ribosylation is a dynamic post-translational modification (PTM) with important roles in cell signalling. This modification occurs on a wide variety of amino acids, and one of the canonical modification sites within proteins is the side chain of glutamic acid. Given the transient nature of this modification (acylal linkage) and the high sensitivity of ADP-ribosylated glutamic acid, stabilized isosteres are required for structural and biochemical studies. Here, we report the synthesis of a mimic of ADP-ribosylated peptide derived from histone H2B that contains carba-ADP-ribosylated glutamine as a potential mimic for Glu-ADPr. We synthesized a cyclopentitol-ribofuranosyl derivative of 5'-phosphoribosylated Fmoc-glutamine and used this in the solid-phase synthesis of the carba-ADPr-peptide mimicking the ADP-ribosylated N-terminal tail of histone H2B. Binding studies with isothermal calorimetry demonstrate that the macrodomains of human MacroD2 and TARG1 bind to carba-ADPr-peptide in the same way as ADPr-peptides containing the native ADP-riboside moiety connected to the side chain of glutamine in the same peptide sequence.

Illuminating Neuropeptide Y Y4 Receptor Binding: Fluorescent Cyclic Peptides with Subnanomolar Binding Affinity as Novel Molecular Tools.

The neuropeptide Y (NPY) Y4 receptor (Y4R), a member of the family of NPY receptors, is physiologically activated by the linear 36-amino acid peptide pancreatic polypeptide (PP). The Y4R is involved in the regulation of various biological processes, most importantly pancreatic secretion, gastrointestinal motility, and regulation of food intake. So far, Y4R binding affinities have been mostly studied in radiochemical binding assays. Except for a few fluorescently labeled PP derivatives, fluorescence-tagged Y4R ligands with high affinity have not been reported. Here, we introduce differently fluorescence-labeled (Sulfo-Cy5, Cy3B, Py-1, Py-5) Y4R ligands derived from recently reported cyclic hexapeptides showing picomolar Y4R binding affinity. With pKi values of 9.22-9.71 (radioligand competition binding assay), all fluorescent ligands (16-19) showed excellent Y4R affinity. Y4R saturation binding, binding kinetics, and competition binding with reference ligands were studied using different fluorescence-based methods: flow cytometry (Sulfo-Cy5, Cy3B, and Py-1 label), fluorescence anisotropy (Cy3B label), and NanoBRET (Cy3B label) binding assays. These experiments confirmed the high binding affinity to Y4R (equilibrium pKd: 9.02-9.9) and proved the applicability of the probes for fluorescence-based Y4R competition binding studies and imaging techniques such as single-receptor molecule tracking.

Structure-based investigation of pyruvate dehydrogenase kinase-3 inhibitory potential of thymoquinone, targeting lung cancer therapy

Protein kinases are an attractive therapeutic target for cardiovascular, cancer and neurodegenerative diseases. Cancer cells demand energy generation through aerobic glycolysis, surpassing “oxidative phosphorylation” (OXPHOS) in mitochondria. The pyruvate dehydrogenase kinases (PDKs) have many regulatory roles in energy generation balance by controlling the pyruvate dehydrogenase complex. Overexpression of PDKs is associated with the overall survival of cancer. PDK3, an isoform of PDK is highly expressed in various cancer types, is targeted for inhibition in this study. PDK3 has been shown to binds strongly with a natural compound, thymoquinone (TQ), which is known to exhibit anti-cancer potential. Detailed interaction between the PDK3 and TQ was carried out using spectroscopic and docking methods. The overall changes in the protein's structures after TQ binding were estimated by UV–Vis spectroscopy, circular dichroism and fluorescence binding studies. The kinase activity assay was also carried out to see the kinase inhibitory potential of TQ. The enzyme inhibition assay suggested an excellent inhibitory potential of TQ towards PDK3 (IC50 = 5.49 μM). We observed that TQ forms a stable complex with PDK3 without altering its structure and can be a potent PDK3 inhibitor which may be implicated in cancer therapy after desired clinical validation.

Quantification of COX-2 Level in Alzheimer's Disease Patients to Develop Potential Blood-Based Biomarker for Early Diagnosis and Therapeutic Target.

Alzheimer's disease (AD) is a progressive neurodegenerative disease and symptoms develop gradually over many years. The current direction for medication development in AD is focused on neuro-inflammation and oxidative stress. Amyloid-β (Aβ) deposition activates microglia leading to neuro-inflammation and neurodegeneration induced by activation of COX-2 via NFκB p50 in glioblastoma cells. The study aimed to evaluate the concentration of COX-2 and NFκB p50 in serum of AD, mild cognitive impairment (MCI), and geriatric control (GC) and to establish a blood-based biomarker for early diagnosis and its therapeutic implications. Proteins and their mRNA level in blood of study groups were measured by surface plasmon resonance (SPR) and quantitative polymerase chain reaction (qPCR), respectively. The level of protein was further validated by western blot. The binding study of designed peptide against COX-2 by molecular docking was verified by SPR. The rescue of neurotoxicity by peptide was also checked by MTT assay on SH-SY5Y cells (neuroblastoma cell line). Proteins and mRNA were highly expressed in AD and MCI compared to GC. However, COX-2 decreases with disease duration. The peptide showed binding affinity with COX-2 with low dissociation constant in SPR and rescued the neurotoxicity of SH-SY5Y cells by decreasing the level of Aβ, tau, and pTau proteins. It can be concluded that COX-2 protein can serve as a potential blood-based biomarker for early detection and can be a good platform for therapeutic intervention for AD.

Diruthenium complexes incorporating carboxylated chalcones with phenyl or ferrocenyl units: Synthesis, structural, electrochemical and DNA binding studies

A total of eight diruthenium sawhorse and cationic complexes incorporating carboxylated chalcones with phenyl or ferrocenyl units have been synthesized and characterized. The electrochemical behavior of the sawhorse and cationic complexes incorporating the ferrocenyl moiety have been studied by cyclic voltammetry. For the cationic complexes both the diruthenium core and the ferrocenyl unit undergo oxidation, in contrast only the ferrocenyl moieties for the sawhorse complexes were oxidized. The enhanced solubility of the cationic complexes over the neutral sawhorse compounds in aqueous medium enabled DNA binding studies to be undertaken for the former. All of the cationic complexes could bind to DNA, and displayed better selectivity for quadruplex over duplex DNA. These results indicate that diruthenium cationic complexes are able to bind to quadruplex DNA and have the potential to function as telomerase inhibitors.

Synthesis, characterization, and BSA binding studies of newfangled 2-phenylacetohydrazide derivatives

Five 2-phenylacetohydrazide derivatives (BPAH = N′-benzylidene-2-phenylacetohydrazide, HBPAH = N’-(2-hydroxybenzylidene)-2-phenylacetohydrazide), PPAH = 2-phenyl-N′-3-phenylallylideneacetohydrazide, FMPAH = N’-(furan-2-ylmethylene)-2-phenylaceto hydrazide and EPAH = N′-ethylidene-2-phenylacetohydrazide were synthesized by the condensation of 2-phenylacetohydrazide with the corresponding aldehyde. The synthesized compounds were characterized by FTIR, 1D, and 2D NMR spectroscopy. The structure of the BPAH and PPAH were analyzed by single crystal X-ray diffraction analysis and in both crystallized compounds, the molecules adopted trans geometry around the –CN- (imine) functional group. To explore the pharmacological significance of these compounds, the binding ability of these compounds with Bovine Serum Albumin (BSA) was investigated using fluorescence spectroscopy. BPAH and PPAH showed the highest binding ability while EPAH, HBPAH, and FMPAH had lower binding ability to BSA molecules. Thermodynamic parameters ΔG, ΔH°, and ΔS° demonstrated that interactions of BSA with compounds BPAH, EPAH, FMAH, and HBPAH were exothermic while for PPAH it was endothermic. The negative enthalpy and entropy of the compounds BPAH, EPAH, FMAH, and HBPAH indicated that van der Waals' forces and hydrogen bonding played a major role in stabilizing the BSA binding with the molecules. Hydrophobic interactions were predominant in the binding of PPAH with BSA tends to interact with two sets of BSA binding sites with an increase in temperature.

Design of inhibitor peptide sequences based on the interfacial knowledge of the protein G-IgG crystallographic complex and their binding studies with IgG.

Protein-protein interactions (PPI) have emerged as valuable targets in medicinal chemistry due to their key roles in important biological processes. The modulation of PPI by small peptides offers an excellent opportunity to develop drugs against human diseases. Here, we exploited the knowledge of the binding interface of the IgG-protein G complex (PDB:1FCC) for designing peptides that can inhibit these complexes. Herein, we have designed several closely related peptides, and the comparison of results from experiments and computational studies indicated that all the peptides bind close to the expected binding site on IgG and the complexes are stable. A minimal sequence consisting of 11 amino acids (P5) with binding constants in the range of 100nM was identified. We propose that the main affinity differences across the series of peptides arose from the presence of polar amino acid residues. Further, the molecular dynamic studies helped to understand the dynamic properties of complexes in terms of flexibility of residues and structural stability at the interface. The ability of P5 to compete with the protein G in recognizing IgG can help in the detection and purification of antibodies. Further, it can serve as a versatile tool for a better understanding of protein-protein interactions.

G-Quadruplex Structure in the ATP-Binding DNA Aptamer Strongly Modulates Ligand Binding Activity.

Secondary structures formed by single-stranded DNA aptamers can allow for the binding of small-molecule ligands. Some of these secondary structures are highly stable in solution and are great candidates for use in the development of molecular tools for biomarker detection, environmental monitoring, and others. In this paper, we explored adenosine triphosphate (ATP)-binding aptamers for the simultaneous detection of two small-molecule ligands: adenosine triphosphate (ATP) and thioflavin T (ThT). The aptamer can form a G-quadruplex (G4) structure with two G-quartets, and our results show that each of these quartets is equally involved in binding. Using fluorescently labeled and label-free methods, we further explored the role of the G4 motif in modulating the ligand binding property of the aptamer by making two extended variants that can form three or four G-quartet G4 structures. Through equilibrium binding and electrospray ionization mass spectrometry (ESI-MS) analysis, we observed a stronger affinity of aptamers to ATP by the variant G4 constructs relative to the native aptamer (Kd range of 0.040-0.042 μM for variants as compared to 0.15 μM for the native ATP aptamer). Additionally, we observed a dual binding of ThT and ATP to the G4 constructs in the label-free and ESI-MS analyses. These findings together suggest that the G4 motif in the ATP aptamer is a critical structural element that is required for optimum ATP binding and can be modulated for the binding of multiple ligands. These findings are instrumental for designing smart molecular tools for a wide range of applications, including biomarker monitoring and ligand binding studies.

Characterization of Type1 Lipid Transfer Protein from Citrus sinensis: Unraveling its potential as an antimicrobial and insecticidal agent

Lipid Transfer Protein1 (LTP1) is a cationic, multifaceted protein belonging to the pathogenesis-related protein (PR14) family. Despite being involved in diverse physiological processes and defense mechanisms, the precise in-vivo role of LTP1 remains undiscovered. This work presents the characterization of recombinant Citrus sinensis LTP1 (CsLTP1) along with lipid binding studies through in-silico and in-vitro approaches. CsLTP1 demonstrated great thermal and pH stability with a huge biotechnological potential. It showed in-vitro binding capacity with jasmonic acid and lipids involved in regulating plant immune responses. Gene expression profiling indicated a significant upregulation of CsLTP1 in Candidatus-infected Citrus plants. CsLTP1 disrupted the cell membrane integrity of various pathogens, making it a potent antimicrobial agent. Further, in-vivo antimicrobial and insecticidal properties of CsLTP1 have been explored. The impact of exogenous CsLTP1 treatment on rice crop metabolism for managing blight disease has been studied using GC–MS. CsLTP1 triggered crucial metabolic pathways in rice plants while controlling the blight disease. CsLTP1 effectively inhibited Helicoverpa armigera larvae by impeding mid-gut α-amylase activity and obstructing its developmental stages. This study highlights the pivotal role of CsLTP1 in plant defense by offering insights for developing multi-target therapeutic agent or disease-resistant varieties to comprehensively tackle the challenges towards crop protection.

Synthesis of a new hydrazone-based schiff base: Spectroscopy, single crystal, DNA binding and theoretical studies

A new thiosemicarbazide-based Schiff base (TSDHB) was synthesized from thiosemicarbazide and 2,3-dihydroxybenzaldehyde. The prepared thiosemicarbazone was characterized by elemental (CHN), FT-IR, 1H and 13C NMR techniques. Furthermore, the molecular structure was probed using the single-crystal X-ray diffraction (SC-XRD) technique, which confirmed the enol tautomeric form with two independent molecules in asymmetric unit. The dissimilarity between the molecular units was determined by molecular overlay plots. The various intermolecular interactions and solid-state assembly stabilization were explored by Hirshfeld surface analysis. Void analysis was executed to examine the mechanical stability of crystalline units. The bioactivity of thiosemicarbazone was probed with the help of its binding capacity with salmon sperm DNA (SS-DNA) by means of the absorption interaction method. Accompanied by biological activity, optoelectronic properties such as nonlinear optical properties of yielded crystal were also explored through the DFT approach at M06/6–311 G (d,p). For this, various kinds of investigations such as frontier molecular orbital (FMO), UV–Vis, global reactivity parameters (GRPs), transition density matrix (TDM), density of states (DOS), natural population analysis (NPA), and natural bond orbital analysis (NBO) were executed at M06 functional. A good agreement was examined between XRD and DFT findings of molecular geometric parameters. Notably, in comparison with urea, TSDHB demonstrated enhanced nonlinear optical properties (linear polarizability=4.766 × 10−23esu and third-order hyperpolarizability=5.939 × 10−35esu). These findings position TSDHB as a promising candidate for DNA binding as well as for photonic materials due to its unique molecular characteristics and enhanced nonlinear optical behavior.

Structure of a novel form of phosphopantetheine adenylyltransferase from Klebsiella pneumoniae at 2.59Å resolution.

Phosphopantetheine adenylyltransferase (EC. 2.7.7.3, PPAT) catalyzes the penultimate step of the multistep reaction in the coenzyme A (CoA) biosynthesis pathway. In this step, an adenylyl group from adenosine triphosphate (ATP) is transferred to 4'-phosphopantetheine (PNS) yielding 3'-dephospho-coenzyme A (dpCoA) and pyrophosphate (PPi). PPAT from strain C3 of Klebsiella pneumoniae (KpPPAT) was cloned, expressed and purified. It was crystallized using 0.1M HEPES buffer and PEG10000 at pH 7.5. The crystals belonged to tetragonal space group P41212 with cell dimensions of a = b = 72.82Å and c = 200.37Å. The structure was determined using the molecular replacement method and refined to values of 0.208 and 0.255 for Rcryst and Rfree factors, respectively. The structure determination showed the presence of three crystallographically independent molecules A, B and C in the asymmetric unit. The molecules A and B are observed in the form of a dimer in the asymmetric unit while molecule C belongs to the second dimer whose partner is related by crystallographic twofold symmetry. The polypeptide chain of KpPPAT folds into a β/α structure. The conformations of the side chains of several residues in the substrate binding site in KpPPAT are significantly different from those reported in other PPATs. As a result, the modes of binding of substrates, phosphopantetheine (PNS) and adenosine triphosphate (ATP) differ considerably. The binding studies using fluorescence spectroscopy indicated a KD value of 3.45 × 10-4M for ATP which is significantly lower than the corresponding values reported for PPAT from other species.

Structural enzymology studies with the substrate 3S-hydroxybutanoyl-CoA: bifunctional MFE1 is a less efficient dehydrogenase than monofunctional HAD.

Multifunctional enzyme, type-1 (MFE1) catalyzes the second and third step of the β-oxidation cycle, being, respectively, the 2E-enoyl-CoA hydratase (ECH) reaction (N-terminal part, crotonase fold) and the NAD+-dependent, 3S-hydroxyacyl-CoA dehydrogenase (HAD) reaction (C-terminal part, HAD fold). Structural enzymological properties of rat MFE1 (RnMFE1) as well as of two of its variants, namely the E123A variant (a glutamate of the ECH active site is mutated into alanine) and the BCDE variant (without domain A of the ECH part), were studied, using as substrate 3S-hydroxybutanoyl-CoA. Protein crystallographic binding studies show the hydrogen bond interactions of 3S-hydroxybutanoyl-CoA as well as of its 3-keto, oxidized form, acetoacetyl-CoA, with the catalytic glutamates in the ECH active site. Pre-steady state binding experiments with NAD+ and NADH show that the kon and koff rate constants of the HAD active site of monomeric RnMFE1 and the homologous human, dimeric 3S-hydroxyacyl-CoA dehydrogenase (HsHAD) for NAD+ and NADH are very similar, being the same as those observed for the E123A and BCDE variants. However, steady state and pre-steady state kinetic data concerning the HAD-catalyzed dehydrogenation reaction of the substrate 3S-hydroxybutanoyl-CoA show that, respectively, the kcat and kchem rate constants for conversion into acetoacetyl-CoA by RnMFE1 (and its two variants) are about 10 fold lower as when catalyzed by HsHAD. The dynamical properties of dehydrogenases are known to be important for their catalytic efficiency, and it is discussed that the greater complexity of the RnMFE1 fold correlates with the observation that RnMFE1 is a slower dehydrogenase than HsHAD.

Conjugate and regiochemical addition of aminoazoles to 2-(4-(2,2-dicyanovinyl)phenoxy)-N-arylacetamide affording fused pyrimidines linked to phenoxy-N-arylacetamide: Antibacterial activity, molecular docking, and DNA binding studies

A facile, and efficient regiochemical synthesis of 7-amino[1,2,4]triazolo[1,5-a]pyrimidine-6-carbonitriles, or 4-aminobenzo[4,5]imidazo[1,2-a]pyrimidine-3-carbonitriles that are linked to phenoxy-N-arylacetamide moieties has been developed. The products are formed via the conjugate additions of exo-NH2 and ring-NH groups of the aminoazoles (3-amino[1,2,4]triazole, and 1H-benzo[d]imidazol-2-amine) to the 2-(4-(2,2-dicyanovinyl)phenoxy)-N-phenylacetamide. Well diffusion method was utilized to assess the antibacterial capabilities of the synthesized compounds (11a-d and 21a-d) against different bacterial strains, and it was found that 21c was the most potent. In accordance with experimental results, the antibacterial molecular docking findings revealed that 21c has remarkable binding capabilities toward different antibiotic-target proteins (PDB IDs: 4H8E, 4C13, 1JIJ, and 1AJ0). Upon investigating the DNA binding characteristics using absorption spectroscopy, the intrinsic binding constant for compound 21c was found to be 2.64 × 104M−1, suggesting that it has a good potential for DNA binding.

Chiral Bis-phosphate Macrocycles for Catalytic, Efficient, and Enantioselective Electrophilic Fluorination.

Incorporation of privileged catalytic scaffolds into a macrocyclic skeleton represents an attractive strategy to furnish supramolecular catalysis systems with enzyme-mimetic cavity and multi-site cooperation. Herein we reported the synthesis, structure, binding properties and catalytic application of a series of chiral bis-phosphate macrocycles toward the challenging asymmetric electrophilic fluorination. With a large, integrated chiral cavity and two cooperative phosphate sites, these macrocycles exhibited good inclusion toward 1,4-diazabicyclo[2.2.2]octane (DABCO) dicationic ammoniums through complementary ion-pair and C-H⋅⋅⋅O interactions, as confirmed by crystallographic and solution binding studies. In fluorocyclization of tryptamines with Selectfluor reagent which has a similar DABCO-based dicationic structure, only 2 mol% macrocycle catalyst afforded the desired pyrroloindoline products in moderate yields and up to 91 % ee. For comparison, the acyclic mono-phosphate analogue gave obviously lower reactivity and enantioselectivity (<20 % ee), suggesting a remarkable macrocyclic effect. The high catalytic efficiency and superior stereocontrol were ascribed to the tight ion-pair binding and cavity-directed noncovalent interaction cooperation.