Hydrophobicity Profile Research Articles

The molecular determinants of calcium ATPase inhibition by curcuminoids

The natural product curcumin and some of its analogs are known inhibitors of the transmembrane enzyme sarco/endoplasmic reticulum calcium ATPase (SERCA). Despite their widespread use, the curcuminoids' binding site in SERCA and their relevant interactions with the enzyme remain elusive. This lack of knowledge has prevented the development of curcuminoids into valuable experimental tools or into agents of therapeutic value. We used the crystal structures of SERCA in its E1 conformation in conjunction with computational tools such as docking and surface screens to determine the most likely curcumin binding site, along with key enzyme/inhibitor interactions. Additionally, we determined the inhibitory potencies and binding affinities for a small set of curcumin analogs. The predicted curcumin binding site is a narrow cleft in the transmembrane section of SERCA, close to the transmembrane/cytosol interface. In addition to pronounced complementarity in shape and hydrophobicity profiles between curcumin and the binding pocket, several hydrogen bonds were observed that were spread over the entire curcumin scaffold, involving residues on several transmembrane helices. Docking-predicted interactions were compatible with experimental observations for inhibitory potencies and binding affinities. Based on these findings, we propose an inhibition mechanism that assumes that the presence of a curcuminoid in the binding site arrests the catalytic cycle of SERCA by preventing it from converting from the E1 to the E2 conformation. This blockage of conformational change is accomplished by a combination of steric hinderance and hydrogen-bond-based cross-linking of transmembrane helices that require flexibility throughout the catalytic cycle.

A Coronin 1-Derived Peptide Inhibits Membrane Fusion by Modulating Membrane Organization and Dynamics.

Membrane fusion is considered the first step in the entry of enveloped viruses into the host cell. Several targeted strategies have been implemented to block viral entry by limiting the fusion protein to form a six-helix bundle, which is a prerequisite for fusion. Nonetheless, the development of broad-spectrum fusion inhibitors is essential to combat emerging and re-emerging viral infections. TG-23, a coronin 1, a tryptophan-aspartate-rich phagosomal protein-derived peptide, demonstrated inhibition of fusion between small unilamellar vesicles (SUVs) by modulating the membrane's physical properties. However, its inhibitory efficacy reduces with an increasing concentration of membrane cholesterol. The present work aims to develop a fusion inhibitor whose efficacy would be unaltered in the presence of membrane cholesterol. A stretch of the tryptophan-aspartic acid-containing peptide with a similar secondary structure and hydrophobicity profile of TG-23 from coronin 1 was synthesized, and its ability to inhibit SUV-SUV fusion with varying concentrations of membrane cholesterol was evaluated. Our results demonstrate that the GG-21 peptide inhibits fusion irrespective of the cholesterol content of the membrane. We have further evaluated the peptide-induced change in the membrane organization and dynamics utilizing arrays of steady-state and time-resolved fluorescence measurements and correlated these results with their effect on fusion. Interestingly, GG-21 displays inhibitory efficacy in a wide variety of lipid compositions despite having a secondary structure and physical properties similar to those of TG-23. Overall, our results advocate that the secondary structure and physical properties of the peptide may not be sufficient to predict its inhibitory efficacy.

Development of a high throughput oxidation profiling strategy for monoclonal antibody products

Oxidation is one of the most common degradation pathways of biopharmaceutics, potentially leading to altered product stability, pharmacokinetics, reduced biological activity and/or an increased immunogenicity. However, it is often insufficiently assessed in early development stages, leaving potential molecule liabilities undiscovered. Aim of the present work was the development of a high throughput oxidation profiling strategy, applicable throughout various stages of biopharmaceutical development. The study demonstrates that the combination of multiple stress assays, including peroxide-based, visible light, and metal-catalyzed oxidation (MCO), enables a comprehensive understanding of a mAb's oxidation susceptibility. The most effective parameters to evaluate oxidation in a high-throughput screening workflow are aggregation, tryptophan oxidation and changes in the hydrophobicity profile of the Fc and Fab subunit measured via Size Exclusion Chromatography, Intrinsic Tryptophan Fluorescence Emission spectroscopy and Reversed-Phase Chromatography subunit analysis, respectively. This oxidation profiling approach is valuable tool to systematically characterize the oxidation susceptibility under relevant conditions, time effective and with minimal sample consumption.

A Simplified Label-Free Method for Proteotyping Sets of Six Isolates in a Single Liquid Chromatography-High-Resolution Tandem Mass Spectrometry Analysis.

Clinical diagnostics and microbiology require high-throughput identification of microorganisms. Sample multiplexing prior to detection is an attractive means to reduce analysis costs and time-to-result. Recent studies have demonstrated the discriminative power of tandem mass spectrometry-based proteotyping. This technology can rapidly identify the most likely taxonomical position of any microorganism, even uncharacterized organisms. Here, we present a simplified label-free multiplexing method to proteotype isolates by tandem mass spectrometry that can identify six microorganisms in a single 20 min analytical run. The strategy involves the production of peptide fractions with distinct hydrophobicity profiles using spin column fractionation. Assemblages of different fractions can then be analyzed using mass spectrometry. Results are subsequently interpreted based on the hydrophobic characteristics of the peptides detected, which make it possible to link each taxon identified to the initial sample. The methodology was tested on 32 distinct sets of six organisms including several worst-scenario assemblages-with differences in sample quantities or the presence of the same organisms in multiple fractions-and proved to be robust. These results pave the way for the deployment of tandem mass spectrometry-based proteotyping in microbiology laboratories.

Molecular mechanism of EAG1 channel inhibition by imipramine binding to the PAS domain

Ether-a-go-go (EAG) channels are key regulators of neuronal excitability and tumorigenesis. EAG channels contain an N-terminal Per-Arnt-Sim (PAS) domain that can regulate currents from EAG channels by binding small molecules. The molecular mechanism of this regulation is not clear. Using surface plasmon resonance and electrophysiology we show that a small molecule ligand imipramine can bind to the PAS domain of EAG1 channels and inhibit EAG1 currents via this binding. We further used a combination of molecular dynamics (MD) simulations, electrophysiology, and mutagenesis to investigate the molecular mechanism of EAG1 current inhibition by imipramine binding to the PAS domain. We found that Tyr71, located at the entrance to the PAS domain cavity, serves as a "gatekeeper" limiting access of imipramine to the cavity. MD simulations indicate that the hydrophobic electrostatic profile of the cavity facilitates imipramine binding and in silico mutations of hydrophobic cavity-lining residues to negatively charged glutamates decreased imipramine binding. Probing the PAS domain cavity-lining residues with site-directed mutagenesis, guided by MD simulations, identified D39 and R84 as residues essential for the EAG1 channel inhibition by imipramine binding to the PAS domain. Taken together, our study identified specific residues in the PAS domain that could increase or decrease EAG1 current inhibition by imipramine binding to the PAS domain. These findings should further the understanding of molecular mechanisms of EAG1 channel regulation by ligands and facilitate the development of therapeutic agents targeting these channels.

Fluorine‐Boosted Kinetic and Selective Molecular Sieving of C6 Derivatives

AbstractPorous molecular sorbents have excellent selectivity towards hydrocarbon separation with energy saving techniques. However, to realize commercialization, molecular sieving processes should be faster and more efficient compared to extended frameworks. In this work, we show that utilizing fluorine to improve the hydrophobic profile of leaning pillararenes affords a substantial kinetic selective adsorption of benzene over cyclohexane (20 : 1 for benzene). The crystal structure shows a porous macrocycle that acts as a perfect match for benzene in both the intrinsic and extrinsic cavities with strong interactions in the solid state. The fluorinated leaning pillararene surpasses all reported organic molecular sieves and is comparable to the extended metal–organic frameworks that were previously employed for this separation such as UIO‐66. Most importantly, this sieving system outperformed the well‐known zeolitic imidazolate frameworks under low pressure, which opens the door to new generations of molecular sieves that can compete with extended frameworks for more sustainable hydrocarbon separation.

Fluorine-Boosted Kinetic and Selective Molecular Sieving of C6 Derivatives.

Porous molecular sorbents have excellent selectivity towards hydrocarbon separation with energy saving techniques. However, to realize commercialization, molecular sieving processes should be faster and more efficient compared to extended frameworks. In this work, we show that utilizing fluorine to improve the hydrophobic profile of leaning pillararenes affords a substantial kinetic selective adsorption of benzene over cyclohexane (20:1 for benzene). The crystal structure shows a porous macrocycle that acts as a perfect match for benzene in both the intrinsic and extrinsic cavities with strong interactions in the solid state. The fluorinated leaning pillararene surpasses all reported organic molecular sieves and is comparable to the extended metal organic frameworks that were previously employed for this separation such as UIO-66. Most importantly, this sieving system outperformed the well-known zeolitic imidazolate frameworks under low pressure, which opens the door to new generations of molecular sieves that can compete with extended frameworks for more sustainable hydrocarbon separation.

Characterization of type I L-asparaginase encoding gene from the thermohalophilic bacterium Bacillus subtilis CAT3.4 from Wawolesea Hot Spring, Southeast Sulawesi, Indonesia

Abstract. Muzuni, Ilham M, Ardiansyah, Suriana, Putri Y, Kartina. 2023. Characterization of type I L-asparaginase encoding gene from the thermohalophilic bacterium Bacillus subtilis CAT3.4 from Wawolesea Hot Spring, Southeast Sulawesi, Indonesia. Biodiversitas 24: 5167-5178. This study aims to determine the molecular characteristics of the gene encoding type 1 L-asparaginase from CAT3.4 thermohalophilic bacterial isolates from the hot springs of Wawolesea, North Konawe, Southeast Sulawesi. This enzyme can be used as a cancer therapy agent and prevents the formation of acrylamide in food products. It is a kind of exploratory research. The characterization was done by amplifying the ansA gene sequence encoding L-asparaginase from CAT3.4 isolate by polymerase chain reactions (PCR) technique using primers AsnBac1-F1 (5'-ACGCGATATTTCTTTTGGCCGG-3') and AsnBac1-R1 (5'-CAGTGAAGAGGTGCATGGTATG-3'). The amplified PCR product was used as a template for sequencing by the Sanger method. The amino acid coding regions (CDS) obtained were bioinformatically characterized using the NCBI website for BLASTn analysis, restriction site and hydrophobicity profiles were analyzed using the BioEdit program, phylogenetic tree was analyzed using the MEGA X program, and type 1 L-asparaginase amino acid sequence was analyzed using the Expasy translate program. The characterization results showed that the target gene has a high similarity to the ansA gene sequence of 20 Bacillus subtilis strains, i.e., 99-100%, is closely related to the ansA gene of Bacillus subtilis strain SRCM103629 and Bacillus subtilis strain GOT9, can be identified using restriction enzymes MluI and BstI to differentiate the species of organisms they produce, has CDS encoding 329 amino acids with a dominant composition of polar amino acids (54.1%) and has a hydrophobicity profile of amino acids dominated by hydrophilic regions. All these characteristics have confirmed that the characterized gene is the ansA gene encoding type 1 L-asparaginase from Bacillus subtilis. The finding of the ansA gene from Bacillus subtilis in a thermohalophilic region in Southeast Sulawesi, Indonesia is a novelty of the research.

Effects of processing technologies on the antioxidant properties of common bean (Phaseolus vulgaris L.) and lentil (Lens culinaris) proteins and their hydrolysates

The effects of ultrasound (280 W, 5 min), heat treatment (75 °C and 90 °C for 10 min) and microfluidization (125 MPa, 4 cycles) as pre or post treatments and their combination with enzymatic hydrolysis on the antioxidant properties of common bean and lentil protein hydrolysates were investigated. In general, hydrolysis resulted in increases of antioxidant activity, both in the presence and absence of processing technologies. The increases reached maximum values of 158% (ABTS), 105% (DPPH), 279% (FRAP) and 107% (TAC) for the bean protein hydrolysates submitted to post-treatment with ultrasound (ABTS, FRAP and TAC) and pre-treatment with microfluidization (DPPH), compared to their respective controls (untreated samples). For lentil proteins, the increases reached 197% (ABTS), 170% (DPPH), 690% (FRAP) and 213% (TAC) for samples submitted to ultrasound post-treatment (ABTS), microfluidization pre-treatment (DPPH) and post-treatment (FRAP), and 75 °C pre-treatment (TAC) compared to their respective controls. Surface hydrophobicity and molecular weight profile by SEC-HPLC analysis indicated modifications in the structures of proteins in function of the different processing technologies. For both proteins, electrophoresis indicated a similar profile for all hydrolysates, regardless of the process applied as pre or post treatment. Solubility of bean and lentil protein concentrates was also improved. These results indicated that different processing technologies can be successfully used in association with enzymatic hydrolysis to improve the antioxidant properties of lentil and bean proteins.

In Silico Post Translational Analysis of Functional Single Nucleotide Alterations in Human TERT Gene Associated with Acute Myeloid Leukemia

Acute myeloid leukemia (AML) refers to a diverse assemblage of hematological malignancies that constitute clonal expansion of immature myeloid progenitor cells in the peripheral blood and bone marrow. TERT gene ensures telomeres maintenance, chromosome stability and prevention of malignancy. The TERT gene has several single nucleotide polymorphisms (SNPs) that have been linked to a number of diseases, including AML. Objective: To classify the harmful TERT gene mutations, and to analyze them using various computational approaches at structural, functional and translational expression levels Methods: National Centre for Biotechnology Information (NCBI) database was used to retrieve nsSNPs of TERT gene (Q53H, V170M, A184T, S255Y, A288V, H412Y, I540M, R631W) reported in AML and they were analyzed using various bioinformatics tools. Results: In this in silico analysis, it was observed that seven out of eight SNPs had a damaging effect; they could affect the protein stability, protein-protein interactions, hydrophobicity, protein folding, three-dimensional structure, secondary structure and conservation profile. 3D models were generated and validated by various tools and the structural effect of these alterations was observed on protein function that was destabilizing to the RNA folding, protein-protein interactions and other functionally associated proteins. Analysis of post translational modifications showed no significant effect of these mutations. Conclusions: These SNPs could be used in future as potential targets in disease diagnosis, biological markers and protein studies.

BIOACTIVE PEPTIDES IN RED MEATS, BYPRODUCTS AND RESIDUES FROM THE MEAT INDUSTRY

O Objective: To provide a comprehensive overview of the generation of bioactive peptides from raw red meat, its by-products, and the waste meat cuts, as well as the bioactive health effects. Design/methodology/approach: A literature search was conducted through the organization and systematized analysis of information for an updated literature review of bioactive peptides in red meat. Results: Meat is a food of great nutritional value for human beings, since the digestibility of its protein stands out. In addition to the nutritional value of this protein, there are some studies in meat where bioactive peptides provide bioactivity mainly as an antihypertensive and antioxidant. Bioactive peptides are generally obtained by enzymatic hydrolysis and through microbial fermentation processes. Subsequently, they are identified by analytical techniques to perform in vitro and in vivo evaluations verifying the bioactivity of the peptides obtained. Limitations on study/implications: The food industry must establish the most reliable methods for generating more reliable peptides to standardize their production and avoid process variability. Findings/conclusions: The bioactive activity to be exerted by the peptides will depend on factors specific to the protein, such as the number of amino acids it contains, the hydrophilic or hydrophobic profile, and size, among others. This information is key to predict the activity the peptide can exert in the human body since many can have multiple activities, the most common being the antioxidant-antihypertensive function.

Crown Ether-Capped Gold Nanoclusters as a Multimodal Platform for Bioimaging.

The distinct polarity of biomolecule surfaces plays a pivotal role in their biochemistry and functions as it is involved in numerous processes, such as folding, aggregation, or denaturation. Therefore, there is a need to image both hydrophilic and hydrophobic bio-interfaces with markers of distinct responses to hydrophobic and hydrophilic environments. In this work, we present a synthesis, characterization, and application of ultrasmall gold nanoclusters capped with a 12-crown-4 ligand. The nanoclusters present an amphiphilic character and can be successfully transferred between aqueous and organic solvents and have their physicochemical integrity retained. They can serve as probes for multimodal bioimaging with light (as they emit near-infrared luminescence) and electron microscopy (due to the high electron density of gold). In this work, we used protein superstructures, namely, amyloid spherulites, as a hydrophobic surface model and individual amyloid fibrils with a mixed hydrophobicity profile. Our nanoclusters spontaneously stained densely packed amyloid spherulites as observed under fluorescence microscopy, which is limited for hydrophilic markers. Moreover, our clusters revealed structural features of individual amyloid fibrils at a nanoscale as observed under a transmission electron microscope. We show the potential of crown ether-capped gold nanoclusters in multimodal structural characterization of bio-interfaces where the amphiphilic character of the supramolecular ligand is required.

Computational and comparative investigation of hydrophobic profile of spike protein of SARS-CoV-2 and SARS-CoV.

The hydrophobic force is one of the most dominant factorsin protein folding. A protein becomes functional only when it achieves its three-dimensional structure and stability upon folding. For a better understanding of the hydrophobic effects and their function in protein folding, quantitative measurement of the hydrophobicity of amino acid side chains is crucial. Spike protein is the primary structural protein in SARS-CoV-2 and SARS-CoV. This study explores how protein sequences in SARS-CoV-2 and SARS-CoV spike proteins encode hydrophobic interactions. Computational tools/techniques have been utilized to investigate the protein sequences of the spike proteins of SARS-CoV-2 and SARS-CoV. Investigations provided an estimate of hydrophobic distribution and its relative strength, indicating a hydrophobic pattern. Analysis of the spike protein's hydrophobic profile may help identify and treat the virus-caused disease; additionally, it can give an insight into the transmissibility and pathogenicity of the virus.

Novel genome sequence of Chinese cavefish (Triplophysa rosa) reveals pervasive relaxation of natural selection in cavefish genomes.

All cavefishes, living exclusively in caves across the globe, exhibit similar phenotypic traits, including the characteristic loss of eyes. To understand whether such phenotypic convergence shares similar genomic bases, here we investigated genome-wide evolutionary signatures of cavefish phenotypes by comparing whole-genome sequences of three pairs of cavefishes and their surface fish relatives. Notably, we newly sequenced and generated a whole-genome assembly of the Chinese cavefish Triplophysa rosa. Our comparative analyses revealed several shared features of cavefish genome evolution. Cavefishes had lower mutation rates than their surface fish relatives. In contrast, the ratio of nonsynonymous to synonymous substitutions (ω) was significantly elevated in cavefishes compared to in surface fishes, consistent with the relaxation of purifying selection. In addition, cavefish genomes had an increased mutational load, including mutations that alter protein hydrophobicity profiles, which were considered harmful. Interestingly, however, we found no overlap in positively selected genes among different cavefish lineages, indicating that the phenotypic convergence in cavefishes was not caused by positive selection of the same sets of genes. Analyses of previously identified candidate genes associated with cave phenotypes supported this conclusion. Genes belonging to the lipid metabolism functional ontology were under relaxed purifying selection in all cavefish genomes, which may be associated with the nutrient-poor habitat of cavefishes. Our work reveals previously uncharacterized patterns of cavefish genome evolution and provides comparative insights into the evolution of cave-associated phenotypic traits.

Symmetrization in the Calculation Pipeline of Gauss Function-Based Modeling of Hydrophobicity in Protein Structures

In this paper, we show, discuss, and compare the effects of symmetrization in two calculation subroutines of the Fuzzy Oil Drop model, a coarse-grained model of density of hydrophobicity in proteins. In the FOD model, an input structure is enclosed in an axis-aligned ellipsoid called a drop. Two profiles of hydrophobicity are then calculated for its residues: theoretical (based on the 3D Gauss function) and observed (based on pairwise hydrophobic interactions). Condition of the hydrophobic core is revealed by comparing those profiles through relative entropy, while analysis of their local differences allows, in particular, determination of the starting location for the search for protein–protein and protein–ligand interaction areas. Here, we improve the baseline workflow of the FOD model by introducing symmetry to the hydrophobicity profile comparison and ellipsoid bounding procedures. In the first modification (FOD–JS), Kullback–Leibler divergence is enhanced with its Jensen–Shannon variant. In the second modification (FOD-PCA), the molecule is optimally aligned with the axes of the coordinate system via principal component analysis, and the size of its drop is determined by the standard deviation of all its effective atoms, making it less susceptible to structural outliers. Tests on several molecules with various shapes and functions confirm that the proposed modifications improve the accuracy, robustness, speed, and usability of Gauss function-based modeling of the density of hydrophobicity in protein structures.

Implementation of immuno-chemoinformatics approaches to construct multi-epitope for vaccine development against Omicron and Delta SARS-CoV-2 variants

BackgroundThe new coronavirus is still a life-threatening menace, because of its changing nature and capacity to produce many mutations to bypass the immune system. The vaccination is the first effective weapon against COVID-19. AimThe study's goal was to design a multi-epitope peptide vaccine (MEPV) for a mix of Omicron and Delta Coronavirus strains using immuno-chemoinformatics tools. MethodsTo create the vaccine epitopes, seven proteins from the Omicron and Delta coronavirus strains were selected (ORF1a, ORF3a, surface protein, membrane protein, ORF7a, ORF8, and nucleocapsid protein). Antigenicity, toxicity, and allergenicity of the epitopes were evaluated. ResultsThe designed vaccine is made up of 534 amino acids that are homogeneous, antigenic, and non-toxic. Sticky restriction enzymes (XhoI and XbaI) were used to incorporate the MEPV into the pmirGLO luciferase vector. SnapGene server was used to create primers for PCR testing. Developing the MEPV is a terrific cost-effective strategy. The created MEPV's physiochemical properties have been determined to be basic, hydrophobic, and stableImmunogenicity and immune response profiles of the developed vaccine candidate were better assessed using in silico immunological simulations. ConclusionsWe advocate moving the built vaccine to the biological validation step, where it may test our findings using appropriate model organisms.

Contrasting Distribution of SARS-CoV-2 Lineages across Multiple Rounds of Pandemic Waves in West Bengal, the Gateway of East and North-East States of India.

ABSTRACTThe evolution of viral variants and their impact on viral transmission have been an area of considerable importance in this pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We analyzed the viral variants in different phases of the pandemic in West Bengal, a state in India that is important geographically, and compared the variants with other states like Delhi, Maharashtra, and Karnataka, located in other regions of the country. We have identified 57 pango-lineages in 3,198 SARS-CoV-2 genomes, alteration in their distribution, as well as contrasting profiles of amino acid mutational dynamics across different waves in different states. The evolving characteristics of Delta (B.1.617.2) sublineages and alterations in hydrophobicity profiles of the viral proteins caused by these mutations were also studied. Additionally, implications of predictive host miRNA binding/unbinding to emerging spike or nucleocapsid mutations were highlighted. Our results throw considerable light on interesting aspects of the viral genomic variation and provide valuable information for improved understanding of wave-defining mutations in unfolding the pandemic.IMPORTANCE Multiple waves of infection were observed in many states in India during the coronavirus disease 2019 (COVID19) pandemic. Fine-scale evolution of major SARS-CoV-2 lineages and sublineages during four wave-window categories: Pre-Wave 1, Wave 1, Pre-Wave 2, and Wave 2 in four major states of India: Delhi (North), Maharashtra (West), Karnataka (South), and West Bengal (East) was studied using large-scale virus genome sequencing data. Our comprehensive analysis reveals contrasting molecular profiles of the wave-defining mutations and their implications in host miRNA binding/unbinding of the lineages in the major states of India.

Multilamellar Liposomes as a Model for Biological Membranes: Saturation Recovery EPR Spin-Labeling Studies.

EPR spin labeling has been used extensively to study lipids in model membranes to understand their structures and dynamics in biological membranes. The lipid multilamellar liposomes, which are the most commonly used biological membrane model, were prepared using film deposition methods and investigated with the continuous wave EPR technique (T2-sensitive spin-labeling methods). These investigations provided knowledge about the orientation of lipids, their rotational and lateral diffusion, and their rate of flip-flop between bilayer leaflets, as well as profiles of membrane hydrophobicity, and are reviewed in many papers and book chapters. In the early 1980s, the saturation recovery EPR technique was introduced to membrane studies. Numerous T1-sensitive spin-label methods were developed to obtain detailed information about the three-dimensional dynamic membrane structure. T1-sensitive methods are advantageous over T2-sensitive methods because the T1 of spin labels (1–10 μs) is 10 to 1000 times longer than the T2, which allows for studies of membrane dynamics in a longer time–space scale. These investigations used multilamellar liposomes also prepared using the rapid solvent exchange method. Here, we review works in which saturation recovery EPR spin-labeling methods were applied to investigate the properties of multilamellar lipid liposomes, and we discuss their relationships to the properties of lipids in biological membranes.

Abstract 6334: In vivo efficacy and toxicity of a reduced potency DNA guanine mono-alkylating ADC payload suitable for the treatment of solid tumors

Abstract Antibody-Drug Conjugates (ADCs) are a growing class of therapeutic agents for the treatment of cancer, with thirteen approved and over 100 others in clinical development. The pyridinobenzodiazepine (PDD) platform is a toolbox of sequence-selective, DNA Guanine mono-alkylating ADC payloads with varying potencies and biophysical properties, enabling a payload-based approach to targeting solid tumours and haematological malignancies. We recently reported the development of a lower potency DNA mono-alkylator, FGX20-75, with substantially superior in vivo properties to other DNA alkylating agents and an efficacy/tolerability profile on-par with a topoisomerase inhibitor-based ADC. This molecule is active in the low nanomolar range (i.e., median potency of 6 nM across a 15 cell-line screen), but is sufficiently hydrophilic to allow efficient conjugation to IgG antibodies with Drug Antobody Ratios (DARs) of up to 7. A maleimide-linked analogue of FGX20-75 has been conjugated to a number of antibodies with a DAR of 4. The ADCs produced exhibit significant in vivo efficacy in human tumour xenograft models. For example, in one case, an ADC targeted to an undisclosed antigen produced complete tumour regressions at 10 mg/kg dosing (Q7dx2) in patient-derived xenograft model of osteosarcoma. A substantially increased tolerability profile compared to other DNA-interactive payloads has been observed (e.g., single dose MED of < 1 mg/kg and MTD in mice of up to 80 mg/kg for a DAR 4 construct). Furthermore, in cynomolgus toxicity studies, a HNSTD has yet to be established at 8 mg/kg. Thus, the increase in loading compared to other DNA-interactive payloads compensates for the drop in potency of FGX20-75, resulting in a potent ADC with substantially increased tolerability and potent efficacy in solid tumours. The favourable hydrophobicity profile of the low potency alkylator FGX20-75, and its ease of conjugation to antibodies, along with the significant in vivo efficacy and tolerability of the ADCs produced from it, suggest that this low potency DNA-alkylating payload represents a promising new approach in the treatment of solid tumours. Citation Format: Paul J. Jackson, Paolo Andriollo, Nicolas Veillard, George Procopiou, David E. Thurston. In vivo efficacy and toxicity of a reduced potency DNA guanine mono-alkylating ADC payload suitable for the treatment of solid tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6334.

Implementation of immuno-chemoinformatics approaches to construct multi-epitope for vaccine development against Omicron and Delta SARS-CoV-2 variants

BackgroundThe new coronavirus is still a life-threatening menace, because of its changing nature and capacity to produce many mutations to bypass the immune system. The vaccination is the first effective weapon against COVID-19. AimThe study's goal was to design a multi-epitope peptide vaccine (MEPV) for a mix of Omicron and Delta Coronavirus strains using immuno-chemoinformatics tools. MethodsTo create the vaccine epitopes, seven proteins from the Omicron and Delta coronavirus strains were selected (ORF1a, ORF3a, surface protein, membrane protein, ORF7a, ORF8, and nucleocapsid protein). Antigenicity, toxicity, and allergenicity of the epitopes were evaluated. ResultsThe designed vaccine is made up of 534 amino acids that are homogeneous, antigenic, and non-toxic. Sticky restriction enzymes (XhoI and XbaI) were used to incorporate the MEPV into the pmirGLO luciferase vector. SnapGene server was used to create primers for PCR testing. Developing the MEPV is a terrific cost-effective strategy. The created MEPV's physiochemical properties have been determined to be basic, hydrophobic, and stableImmunogenicity and immune response profiles of the developed vaccine candidate were better assessed using in silico immunological simulations. ConclusionsWe advocate moving the built vaccine to the biological validation step, where it may test our findings using appropriate model organisms.