Structure-activity Relationship Research Articles

Targeting TYK2 for Fighting Diseases: Recent Advance of TYK2 Inhibitors

Abstract: TYK2 (tyrosine-protein kinase 2) is a non-receptor protein kinase belonging to the JAK family and is closely associated with various diseases, such as psoriasis, inflammatory bowel disease, systemic lupus erythematosus. TYK2 activates the downstream proteins STAT1-5 by participating in the signal transduction of immune factors such as IL-12, IL-23, and IL-10, resulting in immune expression. The activity of the inhibitor TYK2 can effectively block the transduction of excessive immune signals and treat diseases. TYK2 inhibitors are divided into two types of inhibitors according to the different binding sites. One is a TYK2 inhibitor that binds to JH2 and inhibits its activity through an allosteric mechanism. The representative inhibitor is BMS-986165, developed by Bristol-Myers Squibb. The other class binds to the JH1 adenosine triphosphate (ATP) site and prevents the catalytic activity of the kinase by blocking ATP and downstream phosphorylation. This paper mainly introduces the protein structure, signaling pathway, synthesis, structure-activity relationship and clinical research of TYK2 inhibitors.

Recent Advances in Research on Active Compounds Against Hepatic Fibrosis.

Almost all chronic liver diseases cause fibrosis, which can lead to cirrhosis and eventually liver cancer. Liver fibrosis is now considered to be a reversible pathophysiological process and suppression of fibrosis is necessary to prevent liver cancer. At present, no specific drugs have been found that have hepatic anti-fibrotic activity. The research progress of anti-hepatic fibrosis compounds in recent ten years was reviewed to provide a reference for the design and development of anti-hepatic fibrosis drugs. According to the structure of the compounds, they are divided into monocyclic compounds, fused-heterocyclic compounds, and acyclic compounds. In this article, the natural products and synthetic compounds with anti-fibrotic activity in recent ten years were reviewed, with emphasis on their pharmacological activity and structure-activity relationship (SAR). Most of these compounds are natural active products and their derivatives, and there are few researches on synthetic compounds and SAR studies on natural product.

Characterization, antioxidant and α-amylase inhibition of polysaccharides and phosphorylated derivatives from finger citron (Citrus medica L. var. sarcodactylis Swingle)

In this study, the structure-activity relationship of finger citron polysaccharides (FCPs) and their phosphorylated derivatives (P-FCPs) was investigated. Three FCPs (FCP20, FCP40 and FCP60) were successively fractionated by ethanol, and were phosphorylated modification to obtain P-FCPs (P-FCP20, P-FCP40 and P-FCP60). FCPs and P-FCPs are acidic heteropolysaccharides composed of mannose, rhamnose, glucose, galactose, arabinose and galacturonic acid, and exhibited different content of neutral sugar, uronic acid, proteins, polyphenols and sulfates. FTIR and NMR analyses determined the structures of FCPs and P-FCPs, indicating that the phosphorylation modification was successful. P-FCPs possessed the smaller molecular weight distribution and particle size, with significant changes in microstructure than FCPs. Additionally, P-FCPs showed significantly increased antioxidant and α-amylase inhibitory activities compared to FCPs. The inhibitory mechanisms of FCP40 and P-FCP40 on α-amylase was a mixed-type manner and dynamic fluorescence quenching. The results demonstrate that phosphorylation modification can alter the structural features and bioactivities of FCPs, providing an approach for the further development of finger citron in the field of medicinal and functional foods.

Structure-Activity Relationships, Deuteration, and Fluorination of Synthetic Cannabinoid Receptor Agonists Related to AKB48, 5F-AKB-48, and AFUBIATA.

Synthetic cannabinoid receptor agonists (SCRAs) are a growing class of new psychoactive substances (NPS) commonly derived from an N-alkylated indole, indazole, or 7-azaindole scaffold. Diversification of this core (at the 3-position) with amide-linked pendant amino acid groups and modular N-alkylation (of the indole/indazole/7-azaindole core) ensures that novel SCRAs continue to enter the illicit drug market rapidly. In response to the large number of SCRAs that have been detected, pharmacological evaluation of this NPS class has become increasingly common. Adamantane-derived SCRAs have consistently appeared throughout the market since 2011, and as such, a systematic set of these derivatives was synthesized and pharmacologically evaluated. Deuterated and fluorinated adamantane derivatives were prepared to evaluate typical hydrogen bioisosteres, as well as evaluation of the newly detected AFUBIATA.

Alkenyl oxindole is a novel PROTAC moiety that recruits the CRL4DCAF11 E3 ubiquitin ligase complex for targeted protein degradation.

Alkenyl oxindoles have been characterized as autophagosome-tethering compounds (ATTECs), which can target mutant huntingtin protein (mHTT) for lysosomal degradation. In order to expand the application of alkenyl oxindoles for targeted protein degradation, we designed and synthesized a series of heterobifunctional compounds by conjugating different alkenyl oxindoles with bromodomain-containing protein 4 (BRD4) inhibitor JQ1. Through structure-activity relationship study, we successfully developed JQ1-alkenyl oxindole conjugates that potently degrade BRD4. Unexpectedly, we found that these molecules degrade BRD4 through the ubiquitin-proteasome system, rather than the autophagy-lysosomal pathway. Using pooled CRISPR interference (CRISPRi) screening, we revealed that JQ1-alkenyl oxindole conjugates recruit the E3 ubiquitin ligase complex CRL4DCAF11 for substrate degradation. Furthermore, we validated the most potent heterobifunctional molecule HL435 as a promising drug-like lead compound to exert antitumor activity both in vitro and in a mouse xenograft tumor model. Our research provides new employable proteolysis targeting chimera (PROTAC) moieties for targeted protein degradation, providing new possibilities for drug discovery.

Machine Learning-Driven Discovery and Structure–Activity Relationship Analysis of Conductive Metal–Organic Frameworks

Machine Learning-Driven Discovery and Structure–Activity Relationship Analysis of Conductive Metal–Organic Frameworks

Development of semisynthetic saponin immunostimulants

AbstractMany natural saponins demonstrate immunostimulatory adjuvant activities, but they also have some inherent drawbacks that limit their clinical use. To overcome these limitations, extensive structure-activity-relationship (SAR) studies have been conducted. The SAR studies of QS-21 and related saponins reveal that their respective fatty side chains are crucial for potentiating a strong cellular immune response. Replacing the hydrolytically unstable ester side chain in the C28 oligosaccharide domain with an amide side chain in the same domain or in the C3 branched trisaccharide domain is a viable approach for generating robust semisynthetic saponin immunostimulants. Given the striking resemblance of natural momordica saponins (MS) I and II to the deacylated Quillaja Saponaria (QS) saponins (e.g., QS-17, QS-18, and QS-21), incorporating an amide side chain into the more sustainable MS, instead of deacylated QS saponins, led to the discovery of MS-derived semisynthetic immunostimulatory adjuvants VSA-1 and VSA-2. This review focuses on the authors’ previous work on SAR studies of QS and MS saponins.

Coordination assembly and NIR photothermal conversion of Metal-organic framework based on 5-(2-cyanophenoxy) isophthalic acid

The development of new photothermal conversion materials in the field of metal-organic frameworks (MOFs) shows broad prospects, but their design synthesis and proper mechanism analysis are still full of huge challenge. Here, four novel MOFs were constructed with 5-(2-cyanophenoxy) isophthalic acid, {Ni(2-CB-IPA)(bpp)(H2O)}n (1), {Ni2(2-CB-IPA)2(bpa)2(H2O)2}n (2), {Co(2-CB-IPA)(bpp)}n (3), {Mn2(2-CB-IPA)2 (bpp)(H2O)2}n (4). (Where 2-CB-IPA = 5-(2-cyanophenoxy) isophthalic acid, bpa = 1,2-bis(4-pyridine)-ethane; and bpp = 1,3-bis(4-pyridyl)propane). The absorption peak at 730 nm in the near-infrared region indicates that different charge transfer interactions affect the photothermal conversion ability. Under laser irradiation (730 nm, 0.45 W cm−2), such compounds exhibit different and distinct warming processes (1 from 20.8 to 91.8 °C; 2 from 20.1 °C to 86.2 °C; 3 from 20.6 to 77.1 °C) except for compound 4. The excellent crystallinity of these materials after irradiation demonstrates excellent thermal stability and cycling durability. Subsequently, further research on the structure-activity relationship revealed that strong π - π interactions are also the reason for the excellent performance of NIR photothermal conversion of 1 under the premise of high NIR absorption. This work provides a visual platform for the photothermal phenomena of crystalline materials.

Mechanism of targeted adsorption and specific action of bone char on ionic organic pollutants: An analysis based on differences in physicochemical properties

Adsorption is a widely recognized and effective method for treating high-concentration organic industrial wastewater. Bone char (BC) is a promising adsorbent for removing ionic organic pollutants (IOPs) from printing and dyeing wastewater due to its advantageous adsorption properties. To analyze BC's targeted adsorption and specific action mechanism on IOPs, the author first elucidated the physicochemical properties of BC under different preparation conditions. Subsequently, the study compared the targeted adsorption efficacy of BC on various types and molecular structures of IOPs. Through correlation analysis, feature importance analysis, and consideration of the properties of the target substance, the study investigated the targeted adsorption laws of BC for IOPs. Lastly, for substances with specific adsorption characteristics, range analysis, structure–activity relationship analysis, and quantitative analysis of adsorption mechanisms were employed to elucidate the action mechanism of BC. The results indicate that the differences in physicochemical properties (especially CEC and pH) caused by the inorganic mineral components of BC and the number of conjugated double bonds in the molecular structure of IOPs are key factors determining the adsorption effect. Controlling BC's pore structure and electrical conductivity based on the aggregates' conjugated double bonds and particle size can improve adsorption outcomes. The hierarchy of preparation factors influencing the adsorption performance of BC is pyrolysis temperature > particle size > pyrolysis atmosphere. The adsorption of malachite green (MG) by BC primarily involves chemical reactions, including mineral complexation effect (52.38 %), electrostatic interaction (24.76 %), π-π interaction (8.15 %), metal ion exchange (8.12 %), and physical pore filling (6.59 %). It is speculated that the primary interaction mechanism between BC and MG is through cation-π bonds formed between metal cations dissociated from the inorganic mineral components of BC and MG, facilitated by strong electrostatic interaction. The findings offer a theoretical basis for the practical utilization of BC in adsorbing IOPs.

Merging Flow Synthesis and Enzymatic Maturation to Expand the Chemical Space of Lasso Peptides.

Many peptidic natural products, such as lasso peptides, cyclic peptides, and cyclotides, are conformationally constrained and show biological stability, making them attractive scaffolds for drug development. Although many peptides can be synthesized and modified through chemical methods, knot-like lasso peptides such as microcin J25 (MccJ25) and their analogues remain elusive. As the chemical space of MccJ25 analogues accessible through purely biological methods is also limited, we proposed a hybrid approach: flow-based chemical synthesis of non-natural precursor peptides, followed by in vitro transformation with recombinant maturation enzymes, to yield a more diverse array of lasso peptides. Herein, we established the rapid, flow-based synthesis of chemically modified MccJ25 precursor peptides (57 amino acids). Heterologous expression of enzymes McjB and McjC was extensively optimized to improve yields and facilitate the synthesis of multiple analogues of MccJ25, including the incorporation of non-canonical tyrosine and histidine derivatives into the lasso scaffold. Finally, using our chemoenzymatic strategy, we produced a biologically active analogue containing three d-amino acids in the loop region and incorporated backbone N-methylations. Our method provides rapid access to chemically modified lasso peptides that could be used to investigate structure-activity relationships, epitope grafting, and the improvement of therapeutic properties.

Bridged Pt-OH-Mn Mediator in N-coordinated Mn Single Atoms and Pt Nanoparticles for Electrochemical Biomolecule Oxidation and Discrimination.

The rational design of efficient catalysts for uric acid (UA) electrooxidation, as well as the establishment of structure-activity relationships, remains a critical bottleneck in the field of electrochemical sensing. To address these challenges, herein, a hybrid catalyst that integrates carbon-supported Pt nanoparticles and nitrogen-coordinated Mn single atoms (PtNPs/MnNC) is developed. The metal-metal interaction during annealing affords the construction of metallic-bonded Pt-Mn pairs between PtNPs and Mn single atoms, facilitating the electron transfer from PtNPs to the support and thereby optimizing the electronic structure of catalysts. More importantly, experiments and theoretical calculations provide visual proof for the 'incipient hydrous oxide adatom mediator' mechanism for UA oxidation. The Pt-Mn pairs first adsorb OH* to construct the bridged Pt-OH-Mn mediators to serve as a highly active intermediate for N-H bond dissociation and proton transfer. Benefiting from the unique electronic and geometric structure of the catalytic center and reactive intermediates, PtNPs/MnNC exhibits superior electrooxidation performance. The electrochemical sensor based on PtNPs/MnNC enables sensitive detection and discrimination of UA and dopamine in serum samples. This work offers new insights into the construction of novel electrocatalysis for sensitive sensing platforms.

Facile Estimation of Surface Oxygen Vacancies in Co3O4 Catalysts with a Colorimetric Method.

Oxygen vacancy (Ov) is known to act as an active center of the metal oxide. Quantification of surface Ov is vital for understanding the quantitative structure-activity relationship. Facile quantification characterization of surface Ov is highly desirable but still challenging. In this study, we presented a simple colorimetric method for rapidly quantifying surface Ov. As an example of metal oxide nanoparticles, Co3O4 was used to catalyze the 3,3',5,5'-tetramethylbenzidine (TMB)-H2O2 colorimetric reaction. It was found that the absorbance of the TMB-H2O2 system was dependent on the surface Ov amount in Co3O4. The investigation of the mechanism showed that the Ov-dependent absorbance would be attributed to the activity of surface Ov to easily adsorb and dissociate H2O2 into a hydroxyl radical (•OH). The absorbance signal of the TMB-H2O2 system acted as a probe to estimate the surface Ov. This colorimetric measurement could be completed in less than 20 min. The Ov concentrations obtained by the proposed colorimetric method matched well with those obtained by X-ray photoelectron spectroscopy. This method does not require any complex operation and expensive equipment and can be performed in any ordinary chemical laboratory. So, this colorimetric method is expected to become an alternative approach for quantifying the surface Ov in metal oxide nanoparticles. This method will provide essential insights into the rational design and application of Ov.

Assessment of abiotic reduction rates of organic compounds by interpretable structural factors and experimental conditions in anoxic water environments

For organic contaminants in lake sediments, aquifers, and anaerobic bioreactors, their reduction is one of the primary transformation paths in these anoxic water environments. A simple model is introduced to predict pseudo-first order rate constants (kobs) for the abiotic reduction of organic compounds featuring diverse reducible functional groups. It utilizes the largest experimental dataset of –log kobs, encompassing 59 organic compounds (278 data points). Unlike available complex quantitative structure–activity relationship (QSAR) methods, the novel approach requires both experimental conditions and structural parameters. In comparison to one of the available general QSAR methods, the new model demonstrates favorable performance. The average absolute deviation (AAD), absolute maximum deviation (ADmax), average absolute relative deviation (AARD%), and R-squared (R2) values of the estimated outputs for 54/5 training/test data sets of the new model are 0.641/1.761, 1.761/1.417, 20.52/83.87, and 0.797/0.949, respectively. On the other hand, the available general comparative QSAR method shows the AAD: 1.311/2.301, ADmax: 3.795/3.732, AARD%: 641.0/821.2, and R2: 0.003/0.447. For the test set, AAD, AARD%, ADmax, and R2 values for the new/comparative models are 0.649/2.403, 62.20/190.5, 1.215/3.732 and 0.974/0.789, respectively. In summary, the new model offers a straightforward approach for the manual calculation of –log kobs, demonstrating excellent goodness-of-fit, reliability, precision, and accuracy.

3D-QSAR-Directed Synthesis of Halogenated Coumarin-3-Hydrazide Derivatives: Unveiling Their Potential as SDHI Antifungal Agents.

The pursuit of new succinate dehydrogenase (SDH) inhibitors is a leading edge in fungicide research and development. The use of 3D quantitative structure-activity relationship (3D-QSAR) models significantly enhances the development of compounds with potent antifungal properties. In this study, we leveraged the natural product coumarin as a molecular scaffold to synthesize 74 novel 3-coumarin hydrazide derivatives. Notably, compounds 4ap (0.28 μg/mL), 6ae (0.32 μg/mL), and 6ah (0.48 μg/mL) exhibited exceptional in vitro effectiveness against Rhizoctonia solani, outperforming the commonly used fungicide boscalid (0.52 μg/mL). Furthermore, compounds 4ak (0.88 μg/mL), 6ae (0.61 μg/mL), 6ah (0.65 μg/mL), and 6ak (1.11 μg/mL) showed significant activity against Colletotrichum orbiculare, surpassing both the SDHI fungicide boscalid (43.45 μg/mL) and the broad-spectrum fungicide carbendazim (2.15 μg/mL). Molecular docking studies and SDH enzyme assays indicate that compound 4ah may serve as a promising SDHI fungicide. Our ongoing research aims to refine this 3D-QSAR model further, enhance molecular design, and conduct additional bioactivity assays.

Crystal structure of Staphylococcus aureus lipase complex with unsaturated petroselinic acid.

Staphylococcus aureus produces large amounts of toxins and virulence factors. In patients with underlying diseases or compromised immune systems, this bacterium can lead to severe infections and potentially death. In this study, the crystal structure of the complex of S. aureus lipase (SAL), which is involved in the growth of this bacterium, with petroselinic acid (PSA), an inhibitor of unsaturated fatty acids, was determined by X-ray crystallography. Recently, PSA was shown to inhibit S. aureus biofilm formation and the enzymatic activity of SAL. To further characterize the inhibitory mechanism, we determined the half-inhibitory concentration of SAL by PSA and the crystal structure of the complex. The IC50 of the inhibitory effect of PSA on SAL was 3.4 μm. SAL and PSA inhibitors were co-crystallized, and diffraction data sets were collected to 2.19 Å resolution at SPring-8 to determine the crystal structure and elucidate the detailed structural interactions. The results show that the fatty acid moiety of PSA is tightly bound to a hydrophobic pocket extending in two directions around the catalytic residue Ser116. Ser116 was also covalently bonded to the carbon of the unsaturated fatty acid moiety, and an oxyanion hole in SAL stabilized the electrons of the double bond. The difference in inhibitory activity between PSA and ester compounds revealed a structure-activity relationship between SAL and PSA. Additional research is required to further characterize the clinical potential of PSA.

In Silico Prediction of Skin Sensitization for Compounds via Flexible Evidence Combination Based on Machine Learning and Dempster-Shafer Theory.

Skin sensitization is increasingly becoming a significant concern in the development of drugs and cosmetics due to consumer safety and occupational health problems. In silico methods have emerged as alternatives to traditional in vivo animal testing due to ethical and economic considerations. In this study, machine learning methods were used to build quantitative structure-activity relationship (QSAR) models on five skin sensitization data sets (GPMT, LLNA, DPRA, KeratinoSens, and h-CLAT), achieving effective predictive accuracies (correct classification rates of 0.688-0.764 on test sets). To address the complex mechanisms of human skin sensitization, the Dempster-Shafer theory was applied to merge multiple QSAR models, resulting in an evidence-based integrated decision model. Various evidence combinations and combination rules were explored, with the self-defined Q3 rule showing superior balance. The combination of evidence such as GPMT and KeratinoSens and h-CLAT achieved a correct classification rate (CCR) of 0.880 and coverage of 0.893 while maintaining the competitiveness of other combinations. Additionally, the Shapley additive explanations (SHAP) method was used to interpret important features and substructures related to skin sensitization. A comparative analysis of an external human test set demonstrated the superior performance of the proposed method. Finally, to enhance accessibility, the workflow was implemented into a user-friendly software named HSkinSensDS.

Investigation of the Single-Particle Scale Structure-Activity Relationship Providing New Insights for the Development of High-Performance Batteries.

As electric vehicles, portable electronic devices and tools have increasingly high requirements for battery energy density and power density, constantly improving battery performance has become a research focus. Accurate measurement of the structure-activity relationship of active materials is the key to advancing the research of high-performance batteries. However, the conventional performance tests of active materials are based on the electrochemical measurement of porous composite electrodes containing active materials, polymer binders, and conductive carbon additives, which cannot establish an accurate structure-activity relationship with the physical characterization of microregions. In this review, in order to promote the accurate measurement and understanding of the structure-activity relationship of materials, the electrochemical measurement and physical characterization of energy storage materials at single-particle scale are reviewed. The potential problems and possible improvement schemes of the single particle electrochemical measurement and physical characterization are proposed. Their potential applications in single particle electrochemical simulation and machine learning are prospected. This review aims to promote the further application of single particle electrochemical measurement and physical characterization in energy storage materials, hoping to achieve three-dimensional unified evaluation of physical characterization, electrochemical measurement, and theoretical simulation at the single particle scale to provide new inspiration for the development of high-performance batteries. This article is protected by copyright. All rights reserved.

Thiazole as an Indispensable Scaffold in Anti‐Leukemic Agents: A Semicentennial Review

AbstractLeukemia affects the body‘s blood‐forming tissues, especially the bone marrow and lymphatic system. Leukemia incidence varies between communities and between pathological kinds. Many treatment modalities exist for leukemia, such as chemotherapy, targeted therapy, radiation therapy, bone marrow transplantation, immunotherapy, and the engineering of immune cells to fight leukemia. Leukemia might be treated with a variety of pharmaceuticals, the most popular of which are imatinib (Gleevec), dasatinib (Sprycel), nilotinib (Tasigna), obinutuzumab (Gazyva), venetoclax (Venclexta), and so on. Thiazole is one of the scaffolds that are actively explored in leukemia. Derivatives having the thiazole nucleus have been surfacing as potent candidates in the treatment of leukemia for quite sometime now, but a consolidated report accumulating all these ventures is absent. Numerous naturally occurring substances, including flavones, alkaloids, anabolic steroids, and vitamin B1 (thiamine), include the basic thiazole molecule. Thiazole derivatives have been researched for their possible therapeutic effects in the treatment of leukemia. Thus, this review comprising reports regarding the effect of different thiazole‐based species in leukemia is a timely effort to the best of our knowledge. This review covers the chronological development of antileukemic thiazole‐based molecules, their synthesis, biological activity, and structure–activity relationships.

Reducing Overpotential of Lithium-Oxygen Batteries by Diatomic Metal Catalyst Orbital Matching Strategy.

Aprotic Li-O2 batteries have sparked attention in recent years due to their ultrahigh theoretical energy density. Nevertheless, their practical implementation is impeded by the sluggish reaction kinetics at the cathode. Comprehending the catalytic mechanisms is pivotal to developing efficient cathode catalysts for high-performance Li-O2 batteries. Herein, the intrinsic activity map of Li-O2 batteries is established based on the specific adsorption mode of O2 induced by diatomic catalyst orbital matching and the transfer-acceptance-backdonation mechanism, and the four-step screening strategy based on the intrinsic activity map is proposed. Guided by the strategy, FeNi@NC and FeCu@NC promising durable stability with a low overpotential are screened out from 27 Fe-Metal diatomic catalysts. Our research not only provides insights into the fundamental understanding of the reaction mechanism of Li-O2 batteries but also accelerates the rational design of efficient Li-O2 batteries based on the structure-activity relationship.

Synthesis and evaluation of pyridine-3-carboxamide analogs as effective agents against bacterial wilt in tomatoes

This study focused on developing novel pyridine-3-carboxamide analogs to treat bacterial wilt in tomatoes caused by Ralstonia solanacearum. The analogs were synthesized through a multistep process and their structures confirmed using spectroscopy. Molecular docking studies identified the most potent analog from the series. A specific analog, compound 4a, was found to significantly enhance disease resistance in tomato plants infected with R. solanacearum. The structure–activity relationship analysis showed the positions and types of substituents on the aromatic rings of compounds 4a–i strongly influenced their biological activity. Compound 4a, with a chloro group at the para position on ring C and hydroxyl group at the ortho position on ring A, was exceptionally effective against R. solanacearum. When used to treat seeds, the analogs displayed remarkable efficacy, especially compound 4a which had specific activity against bacterial wilt pathogens. Compound 4a also promoted vegetative and reproductive growth of tomato plants, increasing seed germination and seedling vigor. In plants mechanically infected with bacteria, compound 4a substantially reduced the percentage of infection, pathogen quantity in young tissue, and disease progression. The analogs were highly potent due to their amide linkage. Molecular docking identified the best compounds with strong binding affinities. Overall, the strategic design and synthesis of these pyridine-3-carboxamide analogs offers an effective approach to targeting and controlling R. solanacearum and bacterial wilt in tomatoes.