Structure-activity Relationship Studies Research Articles

Discovery of Selective PDE1 Inhibitors with Anti-pulmonary Fibrosis Effects by Targeting the Metal Pocket.

Idiopathic pulmonary fibrosis (IPF) is a fatal lung disease with no ideal drugs. Our previous research demonstrated that phosphodiesterase 1 (PDE1) could be a promising target for the treatment of IPF. However, only a few selective PDE1 inhibitors are available, and the mechanism of recognition between inhibitors and the PDE1 protein is not fully understood. This study carried out a step-by-step optimization of a dihydropyrimidine hit Z94555858. By targeting the metal pocket of PDE1, a lead compound 3f was obtained, exhibiting an IC50 value of 11 nM against PDE1, moderate selectivity over other PDEs, and significant anti-fibrotic effects in bleomycin-induced pulmonary fibrosis rats. The structure-activity relationship study aided by molecular docking revealed that forming halogen bonds with water in the metal pocket greatly enhanced the PDE1 inhibition, providing a novel strategy for further rational design of PDE1 inhibitors.

Structure-activity relationship studies of ME1111, a novel antifungal agent for topical treatment of onychomycosis.

Onychomycosis is a prevalent disease in many areas of the world, affecting approximately 5.5% of the global population. Among several subtypes of onychomycosis, distal-lateral-subungual onychomycosis is the most common, and topical onychomycosis agents effective against this pathogenesis require properties such as high nail penetration and low affinity for keratin, the main component of the nail. To develop novel and highly effective antifungal agents with such properties, we first established an efficient ex vivo evaluation method using bovine hoof slices and human nails, and then used this method to screen an in-house compound library. Using this strategy, we identified 1, a structure with a phenyl-pyrazole skeleton. In subsequent analyses, we investigated the structure-activity relationship of 1, permitting the identification of 28 (Development Code ME1111).

Discovery of highly potent and ALK2/ALK1 selective kinase inhibitors using DNA-encoded chemistry technology

Activin receptor type 1 (ACVR1; ALK2) and activin receptor like type 1 (ACVRL1; ALK1) are transforming growth factor beta family receptors that integrate extracellular signals of bone morphogenic proteins (BMPs) and activins into Mothers Against Decapentaplegic homolog 1/5 (SMAD1/SMAD5) signaling complexes. Several activating mutations in ALK2 are implicated in fibrodysplasia ossificans progressiva (FOP), diffuse intrinsic pontine gliomas, and ependymomas. The ALK2 R206H mutation is also present in a subset of endometrial tumors, melanomas, non-small lung cancers, and colorectal cancers, and ALK2 expression is elevated in pancreatic cancer. Using DNA-encoded chemistry technology, we screened 3.94 billion unique compounds from our diverse DNA-encoded chemical libraries (DECLs) against the kinase domain of ALK2. Off-DNA synthesis of DECL hits and biochemical validation revealed nanomolar potent ALK2 inhibitors. Further structure-activity relationship studies yielded center for drug discovery (CDD)-2789, a potent [NanoBRET (NB) cell IC50: 0.54 μM] and metabolically stable analog with good pharmacological profile. Crystal structures of ALK2 bound with CDD-2281, CDD-2282, or CDD-2789 show that these inhibitors bind the active site through Van der Waals interactions and solvent-mediated hydrogen bonds. CDD-2789 exhibits high selectivity toward ALK2/ALK1 in KINOMEscan analysis and NB K192 assay. In cell-based studies, ALK2 inhibitors effectively attenuated activin A and BMP-induced Phosphorylated SMAD1/5 activation in fibroblasts from individuals with FOP in a dose-dependent manner. Thus, CDD-2789 is a valuable tool compound for further investigation of the biological functions of ALK2 and ALK1 and the therapeutic potential of specific inhibition of ALK2.

Concise Affinity-Based Purification of Ligated mRNA for Structure-Activity Relationship Studies ofNucleosugar Modification Patterns.

Position-specific nucleoside sugar modifications have been shown to improve the translational activity and stability of chemically synthesized mRNA. For pharmaceutical applications of chemically modified mRNA, a rapid purification methodology is imperative to identify the optimal modification pattern. However, while the chemical synthesis of mRNAs can be accomplished by splint ligation of oligonucleotide fragments, the current purification method for ligated mRNAs based on denaturing polyacrylamide gel electrophoresis tends to be time consuming. In this study, we developed a two-step affinity purification method for rapid sample preparation. In this method, ligated mRNA is captured by oligo dT magnetic beads and streptavidin magnetic beads with 3'-biotinylated oligo DNA, which are complementary to the 3'-poly(A) and 5' terminal sequences of the target mRNA, respectively. Therefore, the target mRNA can be isolated from a complex mixture of splint ligations. Using this method, six sugar-modified mRNAs were simultaneously purified, and the translational activities of these mRNAs were evaluated immediately after purification. The results demonstrate that this methodology is suitable for the rapid preparation of various chemically synthesized mRNAs to identify their optimal modification patterns.

Structure-Activity Relationship Studies on Scytophycin B, a Spiro-Epoxide-Containing Cytotoxic Macrolide.

The macrolactone and side-chain fragments of scytophycin B were synthesized and their biological activities evaluated. The highlights of the synthesis for the side-chain and macrolactone fragments were the dimerization approach using cross-metathesis and the late-stage functionalization using Sharpless epoxidation. The cytotoxicity of each fragment was significantly weaker than that of scytophycin B itself, indicating that the whole structure is essential to achieve scytophycin B's potent cytotoxicity.

Discovery of a Novel Macrocyclic Noncovalent CDK7 Inhibitor for Cancer Therapy.

Cyclin-dependent kinase 7 (CDK7) is a key regulator of the cell cycle and transcription, making it a promising target for cancer therapy. Although current CDK7 inhibitors have improved in their selectivity and druglike properties, CDK7 inhibitors have failed to progress through clinical development due to severe gastrointestinal and hematotoxic side effects. To mitigate these limitations, we have developed novel, macrocyclic, noncovalent CDK7 hit compounds 2 and 3 using a macrocyclization platform that has optimized these compounds from SY-5609, a leading clinical asset. We conducted extensive structure-activity relationship (SAR) studies to improve their potency, enhance oral bioavailability, and reduce intestinal distribution, which resulted in compound 13. Compound 13 exhibits potent in vitro activity, good ADME properties, and robust in vivo antitumor activity in xenograft models as a monotherapy. Notably, compound 13 with lower basicity demonstrated improved Caco-2 permeability, reduced blood/plasma ratio, and reduced intestinal distribution in rats, thus mitigating gastrointestinal and hematotoxic side effects.

Comprehensive Insight into Green Synthesis Approaches, Structural Activity Relationship, and Therapeutic Potential of Pyrazolic Chalcone Derivative.

Pyrazolic chalcone exhibits diverse therapeutic activities, including anti-inflammatory, antioxidant, antimicrobial, antitumor, and anti-diabetic properties. Structural activity relationship (SAR) studies play a crucial role in understanding the molecular aspects governing their biological effects, guiding the rational design of derivatives with enhanced efficacy and reduced side effects. This review provides an overview of pyrazolic chalcone derivatives, emphasizing their synthesis through both conventional and green methods. In comparison, conventional synthesis methods have been widely employed in the past for the production of pyrazolic chalcones, often relying on traditional chemical processes that may involve the use of hazardous reagents and generate significant waste. On the other hand, green synthesis methods, in harmony with the growing emphasis on sustainable practices in drug discovery, offer a more environmentally friendly alternative. Green synthesis typically involves the use of eco-friendly reagents, solvents, and energy-efficient processes, resulting in reduced environmental impact and improved resource efficiency. Overall, pyrazolic chalcone derivatives represent a promising class of compounds with significant potential for therapeutic applications.

Explainable machine learning models for predicting the acute toxicity of pesticides to sheepshead minnow (Cyprinodon variegatus).

A quantitative structure-activity relationship (QSAR) study was conducted on 313 pesticides to predict their acute toxicity to Sheepshead minnow (Cyprinodon variegatus) by using DRAGON descriptors. Essentials accounting for a reliable model were all considered carefully, giving full consideration to the OECD (Organization for Economic Co-operation and Development) principles for QSAR acceptability in regulation during the model construction and assessment process. Nine variables were selected through the forward stepwise regression method and used as inputs to construct both linear and nonlinear models. The obtained models were validated internally and externally. Generally, machine learning-based methods, namely support vector machine (SVM), random forest (RF), and projection pursuit regression (PPR), perform better than the multiple linear regression (MLR) model. The statistical results (R2 = 0.682-0.933, Q2LOO = 0.604-0.659, Q2F1 = 0.740-0.796, CCC = 0.861-0.882) of the developed models show that they are robust, reliable, reproducible, accurate and predictive. Comparatively, the RF model performs best, giving predictive correlation coefficient Q2 of 0.814, root mean squared error (RMSE) of 0.658 and mean absolute error (MAE) of 0.534 for the test set, respectively. The RF model (as well as SVM and PPR models) was visualized and explained by using the SHapley Additive explanation (SHAP) analysis to enhance its transparency and credibility. In addition, the applicability domain (AD) range of the RF model was characterized by the Williams plot and the tree manifold approximation and projection (TMAP) technology was utilized to illustrate similarity and diversity of the entire data space, to assist in the analysis of the outliers. Activity cliff detection was investigated by using Arithmetic Residuals in K-groups Analysis (ARKA) descriptors. It was found that none of the pesticides was identified as an activity cliff in the training set or a potential prediction cliff in the test set. Therefore, the RF model fulfills each OECD principle in regulation for QSAR models. The research in this work will aid in the in silico QSAR prediction of the acute toxicity to Sheepshead minnow (Cyprinodon variegatus) for untested and new toxic pesticides and can also be extended to other studies.

Molecular modeling aided design, synthesis, and activity evaluation of N-arylindole derivatives as GPR52 agonists

G protein-coupled receptor 52 (GPR52) is considered to be a promising target to improve the symptoms of psychiatric disorders and its agonists are expected to treat schizophrenia without traditional side effects. Several research institutions have reported some small molecule GPR52 agonists, which can be the starting point for rational drug development. In this study, a series of N-arylindole derivatives were designed and synthesized based on 3g according to classical pharmacochemical methods and computer aided drug design (CADD). The designed compounds exhibited good to excellent activities and the structure-activity relationship (SAR) study was explored. The results show that the connection mode between the hydrophilic head (Part I) and the indole ring (Part II) plays an important role in the GPR52 agonist activity. Among these compounds, compounds 16 and 21 have good GPR52 agonist activity (EC50 = 93 nM and 75 nM) and can inhibit hyperactive behavior in mice induced by MK-801 (EC50 =7.94 mg/kg and 6.64 mg/kg). These designed small molecules will provide new options for the development of novel GPR52 agonists.

Recent Advancements in Benzothiazinones (BTZ) Analogs as DprE1 Inhibitor for Potent Antitubercular Therapeutics

AbstractBenzothiazinone analogs have emerged as a promising class of compounds having potent antimycobacterial activity, particularly against Mycobacterium tuberculosis, the pathogen responsible for tuberculosis. This review highlights the development of benzothiazinone analogs as potential antitubercular agents from the beginning to the recent advancement in the past decade. These compounds have shown potent activity, including drug‐resistant strains of Mycobacterium tuberculosis. Structure–activity relationship studies and modifications have improved their efficacy. Benzothiazinone analogs have favorable pharmacokinetic profiles and show promise in preclinical studies. Challenges include addressing resistance mechanisms and ensuring safety. Their unique mode of action and promising properties make them attractive candidates for the battle against drug‐resistant tuberculosis.

Enantiomeric C-6 fluorinated swainsonine derivatives as highly selective and potent inhibitors of α-mannosidase and α-l-rhamnosidase: design, synthesis and structure-activity relationship study

Six C-6 fluorinated d-swainsonine derivatives and their enantiomers have been designed based on initial docking calculations, and synthesized from enantiomeric ribose-derived aldehydes, respectively. Glycosidase inhibition assay of these derivatives with d-swainsonine (1) and l-swainsonine (ent-1) as contrasts found that the C-6 fluorinated d-swainsonine derivatives with C-8 configurations as R (α) showed specific and potent inhibitions of jack bean α-mannosidase (model enzyme of Golgi α-mannosidase II); whereas their enantiomers with C-8 configurations as S (β) were powerful and selective α-l-rhamnosidase inhibitors. Molecular docking calculations found the C-6 fluorinatedd-swainsonine derivatives 21, 24 and 25 with highly coincident binding conformations with d-swainsonine (1) in their interactions with the active site of α-mannosidase (PDB ID: 1HWW). Reliability of the docking results were confirmed by Molecular Dynamics (MD) simulation. Additionally, solid interactions with residues Gln-392 and Tyr-393 in the active site of α-l-rhamnosidase (PDB ID: 3W5N) were proved to be vital for potent α-l-rhamnosidase inhibitions of the l-swainsonine derivatives. The role of C-6 fluorines in swainsonine derivatives well demonstrated the “mimic effect” of fluorine to hydrogen by minimal influence on the binding conformations and effective compensation for any possible lost interactions. This work contributes to a comprehensive understanding of the structure-activity relationship (SAR) of the fluorinated swainsonines and ever reported branched swainsonines, and has laid good foundation for development of more potent α-mannosidase and α-l-rhamnosidase inhibitors.

Discovery of Novel D/L-Camphor Derivatives Containing Oxime Ester as Fungicide Candidates: Antifungal Activity, Structure-Activity Relationship and Preliminary Mechanistic Study

Discovery of Novel D/L-Camphor Derivatives Containing Oxime Ester as Fungicide Candidates: Antifungal Activity, Structure-Activity Relationship and Preliminary Mechanistic Study

Design and Synthesis of Novel Hydrazinyl Thiazoles from Biomass derived Furfurals: Their Molecular Docking, Anti-Cancer, Anti-Oxidant, and Anti-Bacterial Study

This report presents an application of simple and convenient grindstone chemistry to construct a library of pharmaceutically valuable hydrazinyl thiazole moieties using biomass-derived furfurals as key synthons. Significantly, the current green process avoids the use of catalysts and solvents for the desired conversion, achieving good to excellent product yields in a short reaction time. The synthesized compounds were evaluated for their anti-cancer activity against the human breast cancer cell line (MCF-7) using an in vitro MTT assay, which revealed significant antiproliferative activity of compounds 4d and 4e, with IC50 values of 41.06±0.06 and 38.39±0.90 μg/mL, respectively.Further, the in vitro antibacterial activity of the newly synthesized thiazole derivatives and reference drugs was assessed against both gram-negative bacteria, including Escherichia coli, and gram-positive bacteria such as Bacillus subtilis. The current research demonstrates that compounds 4d and 4e exhibit significantly enhanced antibacterial efficacy against pathogenic bacteria, with MIC values >25 μg/mL and >6.25 μg/mL for Escherichia coli, and >25 μg/mL for Bacillus subtilis for both compounds. The DPPH assay revealed that compounds 4a, 4d, and 4e were the most significant, displaying comparatively higher IC50 values of 41.58±1.28, 42.36±0.45 and 42.31±0.73 μg/mL respectively.Furthermore, the synthesized compounds were investigated through molecular docking studies, which were consistent with the in vitro results. The findings were further supported by a structure-activity relationship (SAR) study.

Structure–Activity Relationship Studies of Imidazo[1′,2′:1,6]pyrido[2,3-d]pyrimidine Derivatives to Develop Selective FGFR Inhibitors as Anticancer Agents for FGF19-overexpressed Hepatocellular Carcinoma

The aberrant activation of fibroblast growth factor (FGF) and FGF receptor (FGFR)-mediated signaling pathways are associated with cancer development, including hepatocellular carcinoma (HCC). A novel series of imidazo[1′,2′:1,6]pyrido[2,3-d]pyrimidine, containing an acrylamide covalent warhead, were synthesized as selective FGFR 1-4 inhibitors. Compound 7n was identified as the most potent inhibitor against FGFR1, 2, and 4, with IC50 values of 8/4 nM (FGFR1/2) and 3.8 nM (FGFR4), and the covalent docking analyses suggested that 7n form a covalent adduct with cysteine residue on the hinge or p-loop of FGFR. Compound 7n exhibited a favorable pharmacokinetic profile and significant in vivo antitumor efficacy in human liver cancer xenograft mouse models (xenograft, FGF/FGFR-dependent HCC cells).

Mechanism-based inactivators of sirtuin 5: A focused structure–activity relationship study

Sirtuin 5 (SIRT5) is a lysine deacylase enzyme that cleaves negatively charged ε-N-acyllysine posttranslational modifications, arising from short dicarboxylic acids. Inhibition of SIRT5 has been as a target for treatment of leukemia and breast cancer. In this work, we performed a focused structure–activity relationship study that identified highly potent inhibitors of SIRT5. Examples of these inhibitors were shown by kinetic evaluation to function as mechanism-based inactivators. Masking of a crucial carboxylate functionality in the inhibitors provided prodrugs, which were demonstrated to bind SIRT5 in cells. This work underscores the importance of kinetic characterization of enzyme inhibitors and provides insights for the further optimization of inhibitors of SIRT5 with potential for in vivo applications

Structure activity relationships of antischistosomal N-phenylbenzamides by incorporation of electron-withdrawing functionalities

For the adult Schistosoma mansoni flatworm pathogen, we report further structure activity relationships (SAR) of 19 N-phenylbenzamide analogs. Our previous SAR studies, designed by selecting representative substituents from the Craig plot, identified 9 and 11 which possessed electron-withdrawing groups that benefited potency. This study sought to enhance the potency of this chemotype by incorporating other electron-withdrawing functionalities not studied previously and to overcome the potential pharmacokinetic liabilities associated with the high lipophilicity of frontrunner compounds. Compared to the most potent compound, 9 (EC50 = 80 nM), from our previous work, the most potent compounds in the current study (32 (EC50 = 1.17 µM), 34 (EC50 = 1.64 µM) and 38 (EC50 = 1.16 µM)) were less active although they retained single digit micromolar potency. Furthermore, compound 38 generated a CC50 value of > 20 µM in counter toxicity screens using HEK 293 cells, translating to a wide selectivity index of > 17.

Multicomponent Syntheses Enable the Discovery of Novel Quisinostat-Derived Chemotypes as Histone Deacetylase Inhibitors

In this study, we synthesized and evaluated novel histone deacetylase (HDAC) inhibitors derived from the clinical candidate quisinostat. A library of 16 compounds categorized in three novel chemotypes was rapidly generated using multicomponent reactions (MCRs), enabling efficient structure-activity relationship studies. First, the compounds were evaluated for their activity against the Plasmodium falciparum strains 3D7 and Dd2, the main malaria-causing parasite, identifying compound 18b of the type C series as the most potent. It demonstrated low nanomolar IC50 values (IC50 (3D7) = 0.023 μM; IC50 (Dd2) = 0.047 μM) and high parasite selectivity (SIMRC-5/Pf3D7 > 2174). HDAC inhibition assays confirmed substantial inhibition of the P. falciparum enzyme PfHDAC1 (IC50 = 0.037 μM) as well as of human HDAC1 (IC50 = 0.021 μM) and HDAC6 (IC50 = 0.25 μM). Docking studies suggested distinct binding modes of 18b in P. falciparum and human HDAC1. Additionally, the in vitro anticancer activity was evaluated in Cal27 (head-neck carcinoma), HepG2 (hepatocellular carcinoma), A2780 (ovarian carcinoma), and U87 (glioblastoma) cell lines. Compounds 9b, 9d, and 13f showed potent antiproliferative activity and caspase 3/7 activation, in contrast to 18b. Furthermore, these compounds caused hyperacetylation of histone H3 and α-tubulin, indicating robust cellular target engagement. Overall, in this work we have identified the HDAC inhibitor 18b with selective antiplasmodial and 9b, 9d, and 13f with selective anticancer activities, providing valuable hits for further drug development efforts aimed at creating derivatives with reduced cytotoxicity against non-cancer cells compared to quisinostat.

An Insight into the Structure-Activity Relationship of Benzimidazole and Pyrazole Derivatives as Anticancer Agents.

Cancer is a leading cause of death worldwide, driving the urgent need for new and effective treatments. Benzimidazole and pyrazole derivatives have gained attention for their potential as anticancer agents due to their diverse biological activities. The development of resistance in cancer cells, toxicity concerns, and inconsistent efficacy across different types of cancer are a few of the challenges. To overcome these challenges, optimisation of these nuclei using the structure-activity relationships is necessary. This review aimed to examine various benzimidazole, pyrazole, and their hybrid derivatives by focusing on their structure-activity relationships (SAR) as anticancer agents. Results of the most potent and least potent benzimidazole, pyrazole compounds, and their hybrid derivatives published by researchers were compiled. The findings of different researchers working on benzimidazole and pyrazole nuclei were reviewed and analysed for different targets and cell lines. Moreover, substitutions on different positions of pyrazole, benzimidazole, and their hybrid were summarised to derive an optimised pharmacophore. Based on our analysis of existing studies, we anticipate that this review will guide researchers in creating potent pyrazole, benzimidazole, and hybrid derivatives crucial for combating cancer effectively. Structure-Activity Relationship (SAR) studies can help in developing pyrazolebenzimidazole hybrids that are more powerful and selective in targeting specific aspects of cancer.

In Situ Self-Assembly of Antibody-Rhamnose Complex as a Pre-Targeting Strategy for Enhanced Cancer Immunotherapy.

Enhancing the Fc effector functions of monoclonal antibodies (mAbs) is a proven strategy for improving cancer immunotherapy. In this study, we present a novel pre-targeting approach that integrates host-guest chemistry with an antibody-recruiting concept to create mAbs with superior effector functions. Using rituximab (RTX), a clinically approved anti-CD20 mAb, as our model, we modified RTX by conjugating it with adamantane (Ada) derivatives and various polyethylene glycol (PEG) linkers to produce RTX-Ada conjugates. These conjugates effectively formed RTX-rhamnose (Rha) complexes in situ through self-assembly, driven by host-guest interactions with Rha-modified β-cyclodextrin. This mechanism successfully redirected endogenous anti-Rha antibodies to target cells, enhancing the availability of Fc domains for improved effector functions, including complement-dependent cytotoxicity (CDC). A structure-activity relationship study indicated that the potency of these in situ complexes was significantly influenced by the length of the PEG linker used; shorter PEG linkers correlated with higher CDC activity. Given the variability in endogenous antibody levels among individuals, this strategy presents a flexible and promising platform for enhancing the efficacy of mAb-based cancer immunotherapy.

Targeting the Plasmodium falciparum IspE Enzyme.

The enzyme IspE in Plasmodium falciparum is considered an attractive drug target, as it is essential for parasite survival and is absent in the human proteome. Yet it still has not been addressed by a small-molecule inhibitor. In this study, we conducted a high-throughput screening campaign against the PfIspE enzyme. Our approach toward a PfIspE inhibitor comprises in vitro screening, structure-activity relationship studies, examining the docking position using an AlphaFold model, and finally target verification through probe binding and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis. The newly synthesized probe containing a diazirine and an alkyne moiety (23) allowed us to demonstrate its binding to IspE in the presence of a lysate of human cells (HEK293 cells) and to get evidence that both probe 23 and the best inhibitor of the series (19) compete for the same IspE binding site.