Structure-activity Relationship Research Articles

MDFit: automated molecular simulations workflow enables high throughput assessment of ligands-protein dynamics.

Molecular dynamics (MD) simulation is a powerful tool for characterizing ligand-protein conformational dynamics and offers significant advantages over docking and other rigid structure-based computational methods. However, setting up, running, and analyzing MD simulations continues to be a multi-step process making it cumbersome to assess a library of ligands in a protein binding pocket using MD. We present an automated workflow that streamlines setting up, running, and analyzing Desmond MD simulations for protein-ligand complexes using machine learning (ML) models. The workflow takes a library of pre-docked ligands and a prepared protein structure as input, sets up and runs MD with each protein-ligand complex, and generates simulation fingerprints for each ligand. Simulation fingerprints (SimFP) capture protein-ligand compatibility, including stability of different ligand-pocket interactions and other useful metrics that enable easy rank-ordering of the ligand library for pocket optimization. SimFPs from a ligand library are used to build & deploy ML models that predict binding assay outcomes and automatically infer important interactions. Unlike relative free-energy methods that are constrained to assess ligands with high chemical similarity, ML models based on SimFPs can accommodate diverse ligand sets. We present two case studies on how SimFP helps delineate structure-activity relationship (SAR) trends and explain potency differences across matched-molecular pairs of (1) cyclic peptides targeting PD-L1 and (2) small molecule inhibitors targeting CDK9.

FeCl3 induced sonochemical heteroarylation: Synthesis of meridianin alkaloid analogues for their in silico/in vitro evaluation against SIRT1

Meridianins A − G, the indole based marine alkaloids have displayed a diverse range of biological properties including anti-cancer / anti-tumour activities. Based on reported correlation between anticancer activities and SIRT1 inhibition, the meridianin alkaloid analogues were explored as possible inhibitors of SIRT1. The FeCl3 mediated regioselective heteroarylation under ultrasound irradiation was employed for the synthesis of this class of N-heterocycles. The methodology involved CC bond forming reaction between 2-amino-4-chloropyrimidine and indole to afford a library of desired compounds in varied yield depending on nature of substituent present on the reactant indole. Indeed the product yield was decreased when the NO2 or OH or two chloro groups were present on the indole ring. The usefulness of the current approach was demonstrated via functionalization of one of the synthesized compound i.e. Meridianin G under ultrasound. All the synthesized compounds were characterized by 1H and 13C NMR and MS spectral data. When docked into the SIRT1 in silico, promising interactions with this protein were noted for some of the meridianin analogues synthesized in addition to their probable selectivity towards SIRT1 over SIRT2. The common interacting residues of SIRT1 were found to be VAL412, PHE413, ILE347, ALA262, ILE411, HIS363, GLN345, ASN346, ILE270, PHE273 and PHE297. Indeed, the top four compounds e.g. 3b, 3c, 3d and 3f participated in H-bond interactions through their indole “NH” and the primary amino group with ASN346, HIS363 and VAL412 of SIRT1. Correlating the findings of in silico studies, these compounds showed promising inhibition of SIRT1 in vitro with IC50 ∼2.9–3.7 µM when 3f emerged as the best active molecule. The SAR (Structure-Activity-Relationship) analysis suggested high to good activities for the NO2, Cl, Br or MeO group at C-5 of indole ring (due to participation of these groups in H-bonding interaction as noted during the in silico docking studies) whereas a free NH moiety of the indole ring was essential for activity. The in silico and in vitro studies along with ADME predictions suggested that compound 3b, 3c, 3d and 3f could be of further pharmacological interest.

Substituent effects of Phenanthroline-Derived Phosphine-Oxide extractants on extraction and separation performance towards U(VI)/Th(IV)

Designing and selecting extractants with high selectivity between uranium and thorium, and developing the relevant separation process is one of the key points to realize efficient utilization of nuclear resources in the thorium-uranium nuclear fuel cycle. In this work, we used four phenanthroline-derived phosphine-oxide extractants with different substituents and studied their extraction ability and separation effect on U(VI)/Th(IV) under different conditions. The Et2-BPPhen and Ph2-BPPhen extractants show weak and strong extraction abilities for U(VI) and Th(IV), respectively. The Et-Ph-BPPhen(R,R) and Et-Ph-BPPhen(R,S) extractants could co-extract U(VI) and Th(IV) under high acidity (DU(VI) > 300, DTh(IV) > 40, SFU(VI)/ Th(IV) < 7, 4 M HNO3), and show high selectivity towards U(VI) over Th(IV) at low acidity (SFU(VI)/ Th(IV) > 200, 0.1 M HNO3). Most Th(IV) can be stripped by adjusting the acidity of the aqueous phase, while U(VI) still remains in the organic phase (STh(IV) ＞ 95 %, SU(VI) < 5 %), so as to achieve the step-by-step process for co-extraction and selective separation. Then, the slope analysis and NMR titration (1H and 31P) determined BPPhen ligands could form ML-type complex with U(VI), and can simultaneously form M/L = 1:1 and 1:2 complexes with Th(IV). The stability constants of the metal–ligand complexes were fitted by UV–Vis spectroscopic titration to estimate coordination abilities of four ligands. Finally, the single-crystals of complexes with the structures of [UO2(L)(NO3)2], [Th(L)(NO3)4] and [Th(L)(H2O)2]·4(ClO4), (L = Et2-BPPhen/Et-Ph-BPPhen(R,R)/Et-Ph-BPPhen(R,S)/Ph2-BPPhen) were produced, and their coordination and packing mode were analyzed. This work contributes to revealing the structure–activity relationship of phenanthroline phosphine-oxide extractants and providing a reference for designing new extractants with high U(VI)/Th(IV) separation efficiency.

Manipulating d-band center of bimetallic Sn-alloy coupling with carbon nanofibers for high-performance electrocatalytic production of ammonia from nitrate

The production of ammonia from electrochemical nitrate reduction reaction (NO3RR) has emerged as a highly promising approach to replace the conventional “Haber-Bosch” process, but the research progress of this field is still hindered by the absence of a structure–activity relationship for manipulating catalyst structure to promote its catalytic performance. In this study, we chose TMSn (M=Fe, Co, Ni) alloys as the models to evaluate the electronic structure and their NO3RR activity. Alloying various transition metals with Sn allows to regulate charge distribution, thereby modulating the d-band center of the catalysts and further regulating the catalytic activity of NO3RR. Density functional theory (DFT) simulation predicts that CoSn alloy, with the strongest NO3− adsorption and lowest thermodynamic energy barrier, is potentially considered as a highly efficient NO3RR catalyst. With this theoretical guidance, a series of TMSn alloy catalysts with carbon nanofiber (TMSn-CNF) as a support were synthesized via a two-step electrospinning/carbonization strategy. The CNF as a substrate ensures the excellent cycling performance. As a result, a significantly enhanced NO3RR activity with a NH3 yield rate of 42.20 mg h−1 cm−2 at −0.6 V vs. RHE is achieved on CoSn-CNF compared with NiSn-CNF (13.91 mg h−1 cm−2), FeSn-CNF (13.81 mg h−1 cm−2) and Sn-CNF (6.10 mg h−1 cm−2), superior to most of the previously reported catalysts. We have further constructed an aqueous Zn-NO3− battery using CoSn-CNF as the cathode, achieving a remarkable power density of 5.88 mW cm−2. This battery not only generates large quantity of NH3, but also functions as an effective power source.

Expedient synthesis of 8-membered azasultams: A combined synthetic, DFT, and in vitro study

Herein we describe the novel approach to the synthesis of functionalized ind(az)olo-fused 1,2,4-thiadiazocine 1,1-dioxides through the CSIC (Carbanion-mediated Sulfonate (Sulfonamide) Intermolecular Coupling (Intramolecular Cyclization) reaction strategy. 1,2,4-Thiadiazocine 1,1-dioxides (put simply 8-membered azasultams) are increasingly popular but quite underrepresented in the literature compounds, were prepared in two simple steps and good yield from readily available reagents. Particularly, the alkylation of 7-functionalized ind(az)oles with N-(chloromethyl)-N-methylmethanesulfonamide gave the corresponding N-((1H-ind(az)ol-1-yl)methyl)-N-methylmethane-sulfonamides which underwent base-mediated cyclization affording the target 8-membered azasultams. The method worked well and provided azasultams decorated with a set of synthetically valuable handles. The conducted DFT calculations explained and rationalized the experimental data thus allowing us to formulate the rules of the structure‒activity relationship. Despite the prepared compounds showing weak cytotoxicity against the MDA-MB-231 breast cancer cell line, they are considered novel building blocks and perspective pharmacological templates prone to further optimization.

Quinacridones as a Building Block for Sustainable Gliding Layers on Ice and Snow.

Quinacridone (QA) and 2,9-dimethylquinacridone (DQA) are synthetic substances suitable as a hard, abrasion-resistant, self-organizing gliding layer on ice and snow. For sustainable use, a large number of parameters must be considered to demonstrate that these non-biogenic substances and their by-products and degradation products are harmless to humans and the environment in the quantities released. For this task, available experimental data are used and supplemented for all tautomers by numerous relevant physical, chemical, toxicological and ecotoxicological estimated values based on various Quantitative Structure Activity Relationship (QSAR) methods. On the one hand, the low solubility of QA and DQA leads to stable gliding layers and thus, low abrasion and uptake by plants, animals and humans. On the other hand, the four hydrogen bond forming functional groups per molecule allow nanoparticle decomposition and enzymatic degradation in natural environments. All available data justify a sustainable use of QA and DQA as a gliding layer. The assessment of the toxicological properties is complemented by an investigation of the size and morphology of DQA particles, as well as field tests indicating excellent performance as a gliding layer on snow.

Discovery, Synthesis, and Activity Evaluation of Novel Five-Membered Sulfur-Containing Heterocyclic Nucleosides as Potential Anticancer Agents In Vitro and In Vivo.

A series of novel five-membered sulfur-containing heterocyclic nucleoside derivatives were designed, synthesized, and evaluated for their anticancer activities in vitro and in vivo. The structure-activity relationship studies revealed that some of them showed obvious antitumor activities in several cancer cell lines. Among them, compound 22o exhibited remarkable antiproliferative activity against HeLa cells and was more potent than cisplatin (IC50 = 2.80 vs 7.99 μM). Furthermore, mechanism studies indicated that 22o inhibited cell metastasis, induced cell apoptosis, decreased mitochondrial membrane potential, and activated autophagy through the PI3K-Akt-mTOR signaling pathway. Moreover, drug affinity responsive target stability and the cellular thermal shift assay revealed that 22o targeted RPS6 and inhibited its phosphorylation. Importantly, 22o inhibited the growth of the HeLa xenograft mouse model with a low systemic toxicity. These results indicated that 22o may serve as potent anticancer agents that merit further attention in future anticancer drug discovery.

Photoredox Cascade Catalysts for Solar Hydrogen Production from Sustainable Hydrogen Sources.

Visible-light-driven photocatalytic hydrogen (H2) production has been extensively studied as a clean and sustainable energy resource. Although sacrificial electron donors (SEDs) are commonly used to evaluate photocatalytic activity, their irreversible decomposition forces charge separation, which disrupts the inherent dual productivity of photocatalysis, that is, the formation of both the reduction and oxidation products. To achieve highly efficient photoinduced charge separation without SED decomposition, the layer-by-layer assembly of redox-active photosensitizing dyes and electron mediators through Zr4+-phosphonate bonds has been extensively studied as an artificial mimic of the electron transport chain in natural photosynthesis. This concept paper presents an overview of photoredox cascade catalytic (PRCC) systems comprising multiple Ru(II)-trisbipyridine-type dyes and mediator layers on Pt-loaded TiO2 nanoparticles for H2 production from redox reversible electron donors (RREDs). The PRCC structure-activity relationship for photocatalytic H2 production is briefly discussed in terms of layer thickness, surface structure and modification, and cooperativity with molecular oxidation catalysts. Finally, new insights into the design of efficient dual-production photocatalysts based on the PRCC structure are presented.

Computational screening of metalloporphyrin catalysts for the activation of carbon dioxide

Electrocatalytic CO2 reduction (eCO2R) to value-added chemicals offers a promising route for carbon capture and utilization. Metalloporphyrin (M-POR) is a class of catalysts for eCO2R that has drawn attention due to its tuneable electronic and structural properties. This work presents a computational screening, based on density functional theory calculations, of one of the key steps in the eCO2R: the adsorption of CO2 on 110 M-PORs with varying peripheral ligands, metal centres, and oxidation states, to understand how these factors can influence CO2 activation. A set of criteria was used to shortlist M-PORs based on their ability to lengthen the C–O bond, bend the O–C–O angle, bind CO2, and donate charge from the metal of the M-POR to the carbon of CO2. 16 systems were selected for their potential to activate CO2. These systems predominantly have the electron configuration of the metal centre in the d[6] and d[7] configurations. Natural bond orbital analysis revealed the impact of electron-withdrawing groups in the system, which increases orbital splitting and, consequently, lowers the ability of the M-POR to activate CO2. Second-order perturbation theory analysis confirms that the presence of electron-donating groups in the ligand structure enhances CO2 activation. This work demonstrates the interconnected effect of peripheral ligands, metal centres, and oxidation states in M-PORs on their ability to adsorb and activate CO2, thereby establishing structure-activity relationships within M-PORs.

Discovery of Biphenyl Derivatives to Target Hsp70-Bim Protein-Protein Interaction in Chronic Myeloid Leukemia by Scaffold Hopping Strategy.

Hsp70-Bim protein-protein interaction (PPI) is the most recently identified specific target in chronic myeloid leukemia (CML) therapy. Herein, we developed a new class of Hsp70-Bim PPI inhibitors via scaffold hopping of S1g-10, the most potent Hsp70-Bim PPI inhibitor thus far. Through structure-activity relationship (SAR) study, we obtained a biphenyl scaffold compound JL-15 with a 5.6-fold improvement in Hsp70-Bim PPI suppression (Kd = 123 vs 688 nM) and a 4-fold improvement in water solubility (29.42 vs 7.19 μg/mL) compared to S1g-10. It maintains comparable apoptosis induction capability with S1g-10 against both TKI-sensitive and TKI-resistant CML cell lines in an Hsp70-Bim-dependent manner. Additionally, through SAR, 1H-15N TRSOY-NMR, and molecular docking, we revealed that Lys319 is a "hot spot" in the Hsp70-Bim PPI interface. Collectively, these results provide a novel chemical scaffold and structural insights for the rational design of Hsp70-Bim PPI inhibitors.

Review of the recent advances of pyrazole derivatives as selective COX-2 inhibitors for treating inflammation.

Pyrazole heterocycle is regarded as an extremely significant agent for the therapy of inflammation. Celecoxib, lonazolac, deracoxib, and phenylbutazone are examples of commercially approved pyrazole drugs with COX-2 inhibitory potential for curing inflammation. There have been recently many reviews for the biological significance of pyrazole derivatives. This review talks about pyrazole derivatives with anti-inflammatory activity and also sheds the light on the recent updates on pyrazole research with an emphasis on some synthetic pathways utilized to construct this privileged scaffold and structure activity relationship that accounts for the anti-inflammatory activity in an attempt to pave the opportunity for medicinal chemists to develop novel anti-inflammatory agents with better COX-2 selectivity.

Near-Term Quantum Classification Algorithms Applied to Antimalarial Drug Discovery.

Computational approaches are widely applied in drug discovery to explore properties related to bioactivity, physiochemistry, and toxicology. Over at least the last 20 years, the exploitation of machine learning on molecular data sets has been used to understand the structure-activity relationships that exist between biomolecules and druggable targets. More recently, these methods have also seen application for phenotypic screening data for neglected diseases such as tuberculosis and malaria. Herein, we apply machine learning to build quantum Quantitative Structure Activity Relationship models from antimalarial data sets. There is a continual need for new antimalarials to address drug resistance, and the readily available in vitro data sets could be utilized with newer machine learning approaches as these develop. Furthermore, quantum machine learning is a relatively new method that uses a quantum computer to perform the calculations. First, we present a classical-quantum hybrid computational approach by building a Latent Bernoulli Autoencoder machine learning model for compressing bit-vector descriptors to a size that can be adapted to quantum computers for classification tasks with limited loss of embedded information. Second, we apply our method for feature map compression to quantum classification algorithms, including a completely novel machine learning algorithm with no analogy in classical computers: the Quantum Fourier Transform Classifier. We apply both these approaches to build quantum machine learning models for small-molecule antimalarials with quantum simulation software and then benchmark these quantum models against classical machine learning approaches. While there are many challenges currently facing the development of reliable quantum computers, our results demonstrate that there is potential for the use of this technology in the field of drug discovery.

QSAR, ADMET, molecular docking, and dynamics studies of 1,2,4-triazine-3(2H)-one derivatives as tubulin inhibitors for breast cancer therapy

Breast cancer remains a leading cause of cancer-related deaths among women globally, necessitating the development of more effective therapeutic agents with minimal side effects. This study explores novel 1,2,4-triazine-3(2H)-one derivatives as potential inhibitors of Tubulin, a pivotal protein in cancer cell division, highlighting a targeted approach in cancer therapy. Using an integrated computational approach, we combined quantitative structure–activity relationship (QSAR) modeling, ADMET profiling, molecular docking, and molecular dynamics simulations to evaluate and predict the efficacy and stability of these compounds. Our QSAR models, developed through rigorous statistical analysis, revealed that descriptors such as absolute electronegativity and water solubility significantly influence inhibitory activity, achieving a predictive accuracy (R2) of 0.849. Molecular docking studies identified compounds with high binding affinities, particularly Pred28, which exhibited the best docking score of − 9.6 kcal/mol. Molecular dynamics simulations conducted over 100 ns provided further insights into the stability of these interactions. Pred28 demonstrated notable stability, with the lowest root mean square deviation (RMSD) of 0.29 nm and root mean square fluctuation (RMSF) values indicative of a tightly bound conformation to Tubulin. The novelty of this work lies in its methodological rigor and the integration of multiple advanced computational techniques to pinpoint compounds with promising therapeutic potential. Our findings advance the current understanding of Tubulin inhibitors and open avenues for the synthesis and experimental validation of these compounds, aiming to offer new solutions for breast cancer treatment.

Tailoring Highly Branched Poly(β-amino ester)s for Efficient and Organ-Selective mRNA Delivery.

Development of mRNA therapeutics necessitates targeted delivery technology, while the clinically advanced lipid nanoparticles face difficulty for extrahepatic delivery. Herein, we design highly branched poly(β-amino ester)s (HPAEs) for efficacious organ-selective mRNA delivery through tailoring their chemical compositions and topological structures. Using an "A2+B3+C2" Michael addition platform, a combinatorial library of 219 HPAEs with varied backbone structures, terminal groups, and branching degrees are synthesized. The branched topological structures of HPAEs provide enhanced serum resistance and significantly higher mRNA expression in vivo. The terminal amine structures of HPAEs determine the organ-selectivity of mRNA delivery following systemic administration: morpholine facilitates liver targeting, ethylenediamine favors spleen delivery, while methylpentane enables mRNA delivery to the liver, spleen, and lungs simultaneously. This study represents a comprehensive exploration of the structure-activity relationship governing both the efficiency and organ-selectivity of mRNA delivery by HPAEs, suggesting promising candidates for treating various organ-related diseases.

Cardiac glycosides with cytotoxic activity from the seeds of Thevetia peruviana

Phytochemical investigation on the extract of the seeds of Thevetia peruviana resulted in the isolation of six new cardiac glycosides, namely theveperosides A-F (1–6), including a rare 19-nor-cardenolide (1), together with seven known analogues (7–13). The chemical structures of these compounds were determined based on detailed spectroscopic analysis. The cytotoxic activities of 1–13 were evaluated against MCF-7, HCT-116, HeLa, and HepG2 cancer cell lines, and their structure-activity relationships (SARs) were investigated. Compound 3 exhibited the significant cytotoxic effects with IC50 values ranging from 0.032 to 0.055 μΜ, which could induce HepG2 cells apoptosis in a dose-dependent manner.

Giant ab-Plane Birefringence in Quasi-1D Fibrous Red Phosphorus.

Quasi-one-dimensional (quasi-1D) van der Waals crystal fibrous red phosphorus (RP) exhibits pronounced in-plane optical anisotropy, positioning it as a potential candidate for polarization-related micro-nano devices. Unfortunately, a comprehensive investigation into the complex refractive index of fibrous RP and the structure-activity relationship connecting the distinctive quasi-1D structure with optical anisotropy is currently deficient. Herein, we have collectively determined the complex refractive index of the fibrous RP flakes within the ab-plane through Kramers-Kronig (KK) analysis and theoretical calculation. Notably, the maximum birefringence of fibrous RP reaches 0.642@475 nm with an absolute extinction coefficient of only 0.08, superior to the reported traditional optical crystals and the emerging low-dimensional materials as well. The remarkable birefringence can be attributed to the synergistic influence of the large electronic dipole polarizability, anisotropic electron density distribution and the distortion of stereochemically active lone pair (SCALP). This work demonstrates the potential of fibrous RP for polarization-sensitive devices, illuminating possibilities to exploit novel giant birefringent crystals based on the structure-activity relationship.

Structure-Based Design and Discovery of a Potent and Cell-Active LC3A/B Covalent Inhibitor.

Autophagy is a highly conserved cellular homeostasis maintenance mechanism in eukaryotes. Microtubule-associated protein light chain 3 (LC3) plays a crucial role in autophagy. It has multiple pairs of protein-protein interactions (PPIs) with other proteins, and these PPIs have an effect on the regulation of autophagosome formation and the recruitment of autophagic substrates. In our previous work, a small molecule covalent inhibitor DC-LC3in-D5 which could inhibit LC3A/B PPIs was identified, but a detailed study of structure-activity relationships (SARs) was lacking. Herein, a new molecule LC3in-C42 was discovered utilizing the hybridization of advantageous fragments, whose potency (IC50 = 7.6 nM) had been greatly improved compared with that of DC-LC3in-D5. LC3in-C42 inhibits autophagy at the cellular level and its efficacy far exceeds that of DC-LC3in-D5. Thus far, LC3in-C42 stands as the most potent LC3A/B small molecule inhibitor. LC3in-C42 could serve as a powerful tool for LC3A/B protein and autophagy research.

Novel mandelic acid derivatives containing piperazinyls as potential candidate fungicides against Monilinia fructicola: Design, synthesis and mechanism study

Brown rot of stone fruit, a disease caused by the ascomycete fungus Monilinia fructicola, has caused significant losses to the agricultural industry. In order to explore and discover potential fungicides against M. fructicola, thirty-one novel mandelic acid derivatives containing piperazine moieties were designed and synthesized based on the amide skeleton. Among them, target compound Z31 exhibited obvious in vitro antifungal activity with the EC50 value of 11.8 mg/L, and significant effects for the postharvest pears (79.4 % protective activity and 70.5 % curative activity) at a concentration of 200 mg/L. Antifungal activity for the target compounds was found to be significantly improved by the large steric hindrance of the R1 groups and the electronegative of the piperazines in the molecular structure, according to a three-dimensional quantitative structure–activity relationship (3D-QSAR) analysis. Further mechanism studies have demonstrated that the compound Z31 can disrupt cell membrane integrity, resulting in increased membrane permeability, release of intracellular electrolytes, and affect the normal growth of hyphae. Additional, morphological study also indicated that Z31 may disrupt the integrity of the membrane by inducing generate excess endogenous reactive oxygen species (ROS) and resulting in the peroxidation of cellular lipids, which was further verified by the detection of malondialdehyde (MDA) content. These studies have provided the basis for the creation of novel fungicides to prevent brown rot in stone fruits.

The Unique Structure–Activity Relationship of Porphyrins and Clay Mineral Systems in Modern Applications: A Comprehensive Review

The Unique Structure–Activity Relationship of Porphyrins and Clay Mineral Systems in Modern Applications: A Comprehensive Review

Electrophile Determines Cellular Phenotypes among XPO1-Targeting Small Molecules.

Covalent drug discovery has experienced a renaissance, with numerous electrophilic small molecules recently gaining FDA approval. Many structurally diverse electrophilic small molecules target exportin-1 (XPO1/CRM1) at cysteine 528, including the selective inhibitor of nuclear export (SINE) selinexor, which was FDA-approved as an anticancer agent in 2019. Emerging evidence supports additional pharmacological classes of XPO1 modulators targeting Cys528, including the selective inhibitors of transcriptional activation (SITAs) and probes that induce rapid degradation of XPO1. Here, we analyzed structure-activity relationships across multiple structural series of XPO1 Cys528-targeting probes. We observe that the electrophilic moiety of Cys528-targeting small molecules plays a decisive role in the cellular behavior observed, with subtle changes in electrophile structure being sufficient to convert XPO1-targeting probes to different pharmacological classes. This investigation represents a unique case study in which the electrophile functionality used to target a specific cysteine determines the pharmacological effect among diverse XPO1-targeting small molecules.