A conformation-selective monoclonal antibody against a small molecule-stabilised signalling-deficient form of TNF

Pharmacodynamic components and molecular mechanism of Gastrodia elata Blume in treating hypertension: Absorbed components, network pharmacology analysis, molecular docking and in vivo experimental verification

ETHNOPHARMACOLOGICAL RELEVANCE

Rhizome of Gastrodia elata Blume (RGE) is a valuable traditional Chinese Medicine (TCM) in the clinical practice. The Compendium of Materia Medica records that RGE has the effect of flatting liver wind out. It has sedative, analgesic, hypnotic, anticonvulsant, anti-hypertensive, anti-myocardial ischemia, anti-arrhythmic and anti-platelet aggregation effects. RGE is often used to relieve and treat vertigo, headache, hypertension, convulsions, and epilepsy in TCM clinic for thousands of years. Accumulated evidences have suggested that hypertension disease is related to the renin-angiotensin-aldosterone system (RAAS) disturbance. However, the potential pharmacodynamic components and anti-hypertensive mechanisms of RGE are unclear now.

AIM OF THE STUDY

The active component and mechanism of RGE in treating hypertension were elucidated to strengthen the quality control and development of anti-hypertensive drugs.

MATERIALS AND METHODS

The anti-hypertensive active components of RGE were analyzed by multi-dimensional qualitative analysis method including ethanol extract, in-vitro intestinal absorption, in-vivo plasma. The ultra high performance liquid chromatography-mass spectrometry (UPLC-Q-Exactive MS/MS) analysis technology was adopted to identify these components. Network pharmacology was applied to predicted anti-hypertensive active components, target proteins and pathways. Molecular docking was used to evaluate the potential molecular binding modes between 68 components and nine proteins. Spontaneously hypertensive rats (SHR) model was adopted to evaluate the activity of reducing systolic and diastolic blood pressure (SBP and DBP). Levels of renin, angiotcnsin II (Ang II) and aldosterone (ALD) in serum were determined by Elisa kit. Immunohistochemical were adopted to compare the changes of Ang II receptor 1 (AT1R) protein levels in SHR model and RGE groups.

RESULTS

The multi-dimensional components qualitative analysis method of RGE was established. The results showed that 79, 70 and 30 components were identified in RGE ethanol extract, in-vitro intestinal absorption and in-vivo plasma, respectively. These components were mainly parishins, nucleosides, amino acids, phenolic acids, flavonoids, organic acids et al. Network pharmacology results showed that anti-hypertensive active components were nucleosides and organic acids. It was speculated that RGE could exert its anti-hypertensive effect by regulating aldosterone-regulated sodium reabsorption, renin-angiotensin system pathways and related target proteins. Molecular docking results showed that 21 components including parishins, nucleosides and phenolic acids were potential active components of anti-hypertensive. Taking together, parishin A, B, E, C, D, adenosine, N6-(4-hydroxybenzyl) adenosine, guanosine, ferulic acid were the main anti-hypertensive active components of RGE. Pharmacodynamic results showed that RGE (0.7 g·kg-1) at low dosage could reduce SBP and DBP of SHR in vivo. Meanwhile, RGE (1.4 g·kg-1) markedly reduced the contents of renin, angiotcnsin II and ALD (p < 0.05) of SHR. Immunohistochemical data demonstrated that RGE (0.7 g·kg-1) could downregulate the protein expression of AT1R. In general, RGE can significantly reduce blood pressure of SHR by regulating RAAS.

CONCLUSION

The multi-dimensional components qualitative analysis combining network pharmacology and molecular docking technology provide a new perspective for discovering potential anti-hypertensive components of RGE. RGE possess anti-hypertensive activity by regulating multiple targets of RAAS. Thus, it has the potential to develop into the novel raw material of anti-hypertensive drugs.

Allosteric antibodies: a novel paradigm in drug discovery

Allostery represents a fundamental mechanism in protein regulation, enabling modulation of protein function from sites distal to the active site. While traditionally explored in the context of small molecules, allosteric modulation is gaining traction as a main mode of action in the realm of antibodies, which offer enhanced specificity and reduced toxicity. This review delves into the rapidly growing field of allosteric antibodies, highlighting recent therapeutic advancements and novel druggability avenues. We also explore the potential of these antibodies as innovative tools in drug discovery and discuss contemporary strategies for designing novel allosteric antibodies, leveraging state-of-the-art computational approaches.

First-in-Human Single and Multiple Ascending Dose Studies of Balinatunfib, a Small Molecule Inhibitor of TNFR1 Signaling in Healthy Participants

Oral small molecule inhibitors of tumor necrosis factor alpha (TNFα) are emerging as attractive therapeutic agents for the treatment of various autoimmune diseases. Balinatunfib (SAR441566), a novel oral inhibitor of tumor necrosis factor receptor 1 (TNFR1) signaling, changes the configuration of the soluble TNFα (sTNFα) trimer and prevents its heterotrimerization with TNFR1 but not TNFR2, thereby blocking TNFR1 signaling. Herein, we report the results from a first-in-human (FIH) study that evaluated the safety, pharmacokinetics (PK), and pharmacodynamics (PD) following single ascending doses (SAD) and multiple ascending doses (MAD) of balinatunfib in healthy male participants. Single (5-600 mg) and multiple (100-600 mg total daily dose for up to 14 days) oral doses of balinatunfib were well-tolerated in all participants. Consistent PK data were obtained across the studies, with a median tmax of 2.5-5 hours, a mean terminal half-life of 22-30 hours, and a time to steady state of 5-6 days. A supra-proportional exposure increase was observed in both SAD and MAD studies, which was less pronounced at doses ≥ 180 mg. Food had no relevant effects on the PK characteristics of balinatunfib. As the main PD read-out, complete TNFα occupancy was shown at all tested time points after the treatment started. Balinatunfib, as the first clinically tested oral TNFR1 signal inhibitor, demonstrated a good safety profile along with favorable PK/PD characteristics that allowed both once and twice daily dosing, confirming a successful preclinical-to-clinical translation and guiding dose selection for further clinical efficacy studies.

TNF receptors: Structure-function relationships and therapeutic targeting strategies

Tumor necrosis factor receptors (TNFR1 and TNFR2) play key roles in mediating inflammatory response and cell death signaling, which are associated with autoimmune disorders, neurodegenerative diseases, and cancers. The structure-function relationships of TNF receptors and their ligands determine the activation or inhibition of downstream signaling pathways. Available crystal structures have provided critical insights into the therapeutic targeting strategies of TNF receptors and their signaling networks. In this review, we discuss the potential of targeting receptor-ligand and receptor-receptor interactions in a competitive manner as well as perturbing receptor conformational dynamics through an allosteric mechanism to modulate TNF receptor signaling. We propose that conformational states of TNF receptors can act as a molecular switch in determining their functions and are important therapeutic targets. The knowledge of the structure-function relationships of TNF receptors can be applied to translational high-throughput drug screening and design of novel receptor-specific modulators with enhanced pharmacological properties.

Discovery of Cyclic Peptide Inhibitors Targeted on TNFα-TNFR1 from Computational Design and Bioactivity Verification

Activating tumor necrosis factor receptor 1 (TNFR1) with tumor necrosis factor alpha (TNFα) is one of the key pathological mechanisms resulting in the exacerbation of rheumatoid arthritis (RA) immune response. Despite various types of drugs being available for the treatment of RA, a series of shortcomings still limits their application. Therefore, developing novel peptide drugs that target TNFα-TNFR1 interaction is expected to expand therapeutic drug options. In this study, the detailed interaction mechanism between TNFα and TNFR1 was elucidated, based on which, a series of linear peptides were initially designed. To overcome its large conformational flexibility, two different head-to-tail cyclization strategies were adopted by adding a proline-glycine (GP) or cysteine-cysteine (CC) to form an amide or disulfide bond between the N-C terminal. The results indicate that two cyclic peptides, R1_CC4 and α_CC8, exhibit the strongest binding free energies. α_CC8 was selected for further optimization using virtual mutations through in vitro activity and toxicity experiments due to its optimal biological activity. The L16R mutant was screened, and its binding affinity to TNFR1 was validated using ELISA assays. This study designed a novel cyclic peptide structure with potential anti-inflammatory properties, possibly bringing an additional choice for the treatment of RA in the future.

Targeting the TNF-α-TNFR interaction with EGCG to block NF-κB signaling in human synovial fibroblasts

The tumor necrosis factor alpha (TNF-α)-TNF-α receptor (TNFR) interaction plays a central role in the pathogenesis of various autoimmune diseases, particularly rheumatoid arthritis, and is therefore considered a key target for drug discovery. However, natural compounds that can specifically block the TNF-α-TNFR interaction are rarely reported. (-)-Epigallocatechin-3-gallate (EGCG) is the most active, abundant, and thoroughly investigated polyphenolic compound in green tea. However, the molecular mechanism by which EGCG ameliorates autoimmune arthritis remains to be elucidated. In the present study, we found that EGCG can directly bind to TNF-α, TNFR1, and TNFR2 with similar μM affinity and disrupt the interactions between TNF-α and TNFR1 and TNFR2, which inhibits TNF-α-induced L929 cell death, blocks TNF-α-induced NF-κB activation in 293-TNF-α response cell line, and eventually leads to inhibition of TNF-α-induced NF-κB signaling pathway in HFLS and MH7A cells. Thus, regular consumption of EGCG in green tea may represent a potential therapeutic agent for the treatment of TNF-α-associated diseases.

It's ok to be outnumbered - sub-stoichiometric modulation of homomeric protein complexes

An arsenal of molecular tools with increasingly diversified mechanisms of action is being developed by the scientific community to enable biological interrogation and pharmaceutical modulation of targets and pathways of ever increasing complexity. While most small molecules interact with the target of interest in a 1 : 1 relationship, a noteworthy number of recent examples were reported to bind in a sub-stoichiometric manner to a homomeric protein complex. This approach requires molecular understanding of the physiologically relevant protein assemblies and in-depth characterization of the compound's mechanism of action. The recent literature examples summarized here were selected to illustrate methods used to identify and characterize molecules with such mechanisms. The concept of one small molecule targeting a homomeric protein assembly is not new but the subject deserves renewed inspection in light of emerging technologies and increasingly diverse target biology, to ensure relevant in vitro systems are used and valuable compounds with potentially novel sub-stoichiometric mechanisms of action aren't overlooked.

An orally available small molecule that targets soluble TNF to deliver anti-TNF biologic-like efficacy in rheumatoid arthritis

Tumor necrosis factor (TNF) is a pleiotropic cytokine belonging to a family of trimeric proteins with both proinflammatory and immunoregulatory functions. TNF is a key mediator in autoimmune diseases and during the last couple of decades several biologic drugs have delivered new therapeutic options for patients suffering from chronic autoimmune diseases such as rheumatoid arthritis and chronic inflammatory bowel disease. Attempts to design small molecule therapies directed to this cytokine have not led to approved products yet. Here we report the discovery and development of a potent small molecule inhibitor of TNF that was recently moved into phase 1 clinical trials. The molecule, SAR441566, stabilizes an asymmetrical form of the soluble TNF trimer, compromises downstream signaling and inhibits the functions of TNF in vitro and in vivo. With SAR441566 being studied in healthy volunteers we hope to deliver a more convenient orally bioavailable and effective treatment option for patients suffering with chronic autoimmune diseases compared to established biologic drugs targeting TNF.

Phytochemical Analysis of the Methanolic Extract and Essential Oil from Leaves of Industrial Hemp Futura 75 Cultivar: Isolation of a New Cannabinoid Derivative and Biological Profile Using Computational Approaches

Cannabis sativa L. is a plant belonging to the Cannabaceae family, cultivated for its psychoactive cannabinoid (Δ⁹-THC) concentration or for its fiber and nutrient content in industrial use. Industrial hemp shows a low Δ⁹-THC level and is a valuable source of phytochemicals, mainly represented by cannabinoids, flavones, terpenes, and alkaloids, with health-promoting effects. In the present study, we investigated the phytochemical composition of leaves of the industrial hemp cultivar Futura 75, a monoecious cultivar commercially used for food preparations or cosmetic purposes. Leaves are generally discarded, and represent waste products. We analyzed the methanol extract of Futura 75 leaves by HPLC and NMR spectroscopy and the essential oil by GC-MS. In addition, in order to compare the chemical constituents, we prepared the water infusion. One new cannabinoid derivative (1) and seven known components, namely, cannabidiol (2), cannabidiolic acid (3), β-cannabispirol (4), β-cannabispirol (5), canniprene (6), cannabiripsol (7), and cannflavin B (8) were identified. The content of CBD was highest in all preparations. In addition, we present the outcomes of a computational study focused on elucidating the role of 2α-hydroxy-Δ^3,7-cannabitriol (1), CBD (2), and CBDA (3) in inflammation and thrombogenesis.

Network pharmacology and experimental verification based research into the effect and mechanism of Aucklandiae Radix-Amomi Fructus against gastric cancer

To investigate the mechanism of the Aucklandiae Radix–Amomi Fructus (AR–AF) herb pair in treating gastric cancer (GC) by using network pharmacology and experimental verification. Using the traditional Chinese medicine system pharmacology database and analysis platform (TCMSP), the major active components and their corresponding targets were estimated and screened out. Using Cytoscape 3.7.2 software, a visual network was established using the active components of AR–AF and the targets of GC. Based on STRING online database, the protein interaction network of vital targets was built and analyzed. With the Database for Annotation, Visualization, and Integrated Discovery (DAVID) server, the gene ontology (GO) biological processes and the Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathways of the target enrichment were performed. AutoDock Vina was used to perform molecular docking and calculate the binding affinity. The mRNA and protein expression levels of the hub targets were analyzed by the Oncomine, GEPIA, HPA databases and TIMER online tool, and the predicted targets were verified by qRT–PCR in vitro. Eremanthin, cynaropicrin, and aceteugenol were identified as vital active compounds, and AKT1, MAPK3, IL6, MAPK1, as well as EGFR were considered as the major targets. These targets exerted therapeutic effects on GC by regulating the cAMP signaling pathway, and PI3K-Akt signaling pathway. Molecular docking revealed that these active compounds and targets showed good binding interactions. The validation in different databases showed that most of the results were consistent with this paper. The experimental results confirmed that eremanthin could inhibit the proliferation of AGS by reducing the mRNA expression of hub targets. As predicted by network pharmacology and validated by the experimental results, AR–AF exerts antitumor effects through multiple components, targets, and pathways, thereby providing novel ideas and clues for the development of preparations and the treatment of GC.

Membrane Hormone Receptors and Their Signaling Pathways as Targets for Endocrine Disruptors

The endocrine disruptors are mostly small organic molecules developed for numerous and very diverse industrial applications. They essentially act through nuclear receptors with small and hydrophobic endogenous ligands. Nevertheless, potential adverse effects through membrane hormone receptors cannot be ruled out, and have indeed been observed. The present paper reviews how orthosteric and allosteric binding sites of the different families of membrane receptors can be targets for man-made hydrophobic molecules (components of plastics, paints, flame retardants, herbicides, pesticides, etc.). We also review potential target proteins for such small hydrophobic molecules downstream of membrane receptors at the level of their intracellular signaling pathways. From the currently available information, although endocrine disruptors primarily affect nuclear receptors’ signaling, membrane receptors for hormones, cytokines, neuro-mediators, and growth factors can be affected as well and deserve attention.

Discovery and Mechanism of Action of Small Molecule Inhibitors of Ceramidases

Sphingolipid metabolism is tightly controlled by enzymes to regulate essential processes in human physiology. The central metabolite is ceramide, a pro-apoptotic lipid catabolized by ceramidase enzymes to produce pro-proliferative sphingosine-1-phosphate. Alkaline ceramidases are transmembrane enzymes that recently attracted attention for drug development in fatty liver diseases. However, due to their hydrophobic nature, no specific small molecule inhibitors have been reported. We present the discovery and mechanism of action of the first drug-like inhibitors of alkaline ceramidase 3 (ACER3). In particular, we chemically engineered novel fluorescent ceramide substrates enabling screening of large compound libraries and characterized enzyme:inhibitor interactions using mass spectrometry and MD simulations. In addition to revealing a new paradigm for inhibition of lipid metabolising enzymes with non-lipidic small molecules, our data lay the ground for targeting ACER3 in drug discovery efforts.

Conformation-locking antibodies for the discovery and characterization of KRAS inhibitors

Small molecules that stabilize inactive protein conformations are an underutilized strategy for drugging dynamic or otherwise intractable proteins. To facilitate the discovery and characterization of such inhibitors, we created a screening platform to identify conformation-locking antibodies for molecular probes (CLAMPs) that distinguish and induce rare protein conformational states. Applying the approach to KRAS, we discovered CLAMPs that recognize the open conformation of KRAS^G12C stabilized by covalent inhibitors. One CLAMP enables the visualization of KRAS^G12C covalent modification in vivo and can be used to investigate response heterogeneity to KRAS^G12C inhibitors in patient tumors. A second CLAMP enhances the affinity of weak ligands binding to the KRAS^G12C switch II region (SWII) by stabilizing a specific conformation of KRAS^G12C, thereby enabling the discovery of such ligands that could serve as leads for the development of drugs in a high-throughput screen. We show that combining the complementary properties of antibodies and small molecules facilitates the study and drugging of dynamic proteins.

TNF-α: The shape of small molecules to come?

In 2020, the anti-tumor necrosis factor (TNF) monoclonal antibody Humira® generated US$165.8 billion in cumulative sales and snatched the crown for the industry's most successful drug from Lipitor (atorvastatin). TNF-α is a major component in beneficial and disease-related inflammation and TNF-α-inhibitor biologics have gained widespread use in autoimmune diseases, such as rheumatoid arthritis (RA). Many more diseases could benefit from TNF-α inhibitors, such as Alzheimer's disease (AD) or major depression. However, the nature of TNF-α-inhibitor biologics prohibits central nervous system (CNS) applications. Moreover, high drug production costs and pricing, together with antidrug immune reactions and insufficient patient coverage, argue for the development of small-molecule drugs. Recently, drug-like orally available small molecules were described with high activity in animal disease models with activities comparable to those of antibodies.

Modulating Target Protein Biology Through the Re-mapping of Conformational Distributions Using Small Molecules

Over the last 10 years considerable progress has been made in the application of small molecules to modulating protein-protein interactions (PPIs), and the navigation from "undruggable" to a host of candidate molecules in clinical trials has been well-charted in recent, comprehensive reviews. Structure-based design has played an important role in this scientific journey, with three dimensional structures guiding medicinal chemistry efforts. However, the importance of two additional dimensions: movement and time is only now being realised, as increasing computing power, closely aligned with wet lab validation, is applied to the challenge. Protein dynamics are fundamental to biology and disease, and application to PPI drug discovery has massively widened the scope for new chemical entities to influence function from allosteric, and previously unreported, sites. In this forward-looking perspective we highlight exciting, new opportunities for small molecules to modulate disease biology, by adjusting the frequency profile of natural conformational sampling, through the stabilisation of clinically desired conformers of target proteins.