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1.
Nat Commun ; 15(1): 3883, 2024 May 08.
Article En | MEDLINE | ID: mdl-38719805

The long interspersed nuclear element-1 (LINE-1 or L1) retrotransposon is the only active autonomously replicating retrotransposon in the human genome. L1 harms the cell by inserting new copies, generating DNA damage, and triggering inflammation. Therefore, L1 inhibition could be used to treat many diseases associated with these processes. Previous research has focused on inhibition of the L1 reverse transcriptase due to the prevalence of well-characterized inhibitors of related viral enzymes. Here we present the L1 endonuclease as another target for reducing L1 activity. We characterize structurally diverse small molecule endonuclease inhibitors using computational, biochemical, and biophysical methods. We also show that these inhibitors reduce L1 retrotransposition, L1-induced DNA damage, and inflammation reinforced by L1 in senescent cells. These inhibitors could be used for further pharmacological development and as tools to better understand the life cycle of this element and its impact on disease processes.


Endonucleases , Long Interspersed Nucleotide Elements , Humans , Long Interspersed Nucleotide Elements/genetics , Endonucleases/metabolism , Endonucleases/genetics , Endonucleases/antagonists & inhibitors , Enzyme Inhibitors/pharmacology , Enzyme Inhibitors/chemistry , DNA Damage , Small Molecule Libraries/pharmacology , Small Molecule Libraries/chemistry , Cellular Senescence/drug effects , Deoxyribonuclease I
2.
Int J Mol Sci ; 25(9)2024 Apr 23.
Article En | MEDLINE | ID: mdl-38731811

Recently studied N-(ß-d-glucopyranosyl)-3-aryl-1,2,4-triazole-5-carboxamides have proven to be low micromolar inhibitors of glycogen phosphorylase (GP), a validated target for the treatment of type 2 diabetes mellitus. Since in other settings, the bioisosteric replacement of the 1,2,4-triazole moiety with imidazole resulted in significantly more efficient GP inhibitors, in silico calculations using Glide molecular docking along with unbound state DFT calculations were performed on N-(ß-d-glucopyranosyl)-arylimidazole-carboxamides, revealing their potential for strong GP inhibition. The syntheses of the target compounds involved the formation of an amide bond between per-O-acetylated ß-d-glucopyranosylamine and the corresponding arylimidazole-carboxylic acids. Kinetics experiments on rabbit muscle GPb revealed low micromolar inhibitors, with the best inhibition constants (Kis) of ~3-4 µM obtained for 1- and 2-naphthyl-substituted N-(ß-d-glucopyranosyl)-imidazolecarboxamides, 2b-c. The predicted protein-ligand interactions responsible for the observed potencies are discussed and will facilitate the structure-based design of other inhibitors targeting this important therapeutic target. Meanwhile, the importance of the careful consideration of ligand tautomeric states in binding calculations is highlighted, with the usefulness of DFT calculations in this regard proposed.


Enzyme Inhibitors , Glycogen Phosphorylase , Imidazoles , Molecular Docking Simulation , Kinetics , Rabbits , Animals , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/pharmacology , Enzyme Inhibitors/chemical synthesis , Glycogen Phosphorylase/antagonists & inhibitors , Glycogen Phosphorylase/metabolism , Glycogen Phosphorylase/chemistry , Imidazoles/chemistry , Imidazoles/chemical synthesis , Imidazoles/pharmacology , Computer Simulation , Structure-Activity Relationship , Triazoles/chemistry , Triazoles/pharmacology , Triazoles/chemical synthesis
3.
Int J Mol Sci ; 25(9)2024 Apr 23.
Article En | MEDLINE | ID: mdl-38731830

Brevibacillus sp. JNUCC 41, characterized as a plant-growth-promoting rhizobacterium (PGPR), actively participates in lipid metabolism and biocontrol based on gene analysis. This study aimed to investigate the crucial secondary metabolites in biological metabolism; fermentation, extraction, and isolation were performed, revealing that methyl indole-3-acetate showed the best hyaluronidase (HAase) inhibitory activity (IC50: 343.9 µM). Molecular docking results further revealed that the compound forms hydrogen bonds with the residues Tyr-75 and Tyr-247 of HAase (binding energy: -6.4 kcal/mol). Molecular dynamics (MD) simulations demonstrated that the compound predominantly binds to HAase via hydrogen bonding (MM-PBSA binding energy: -24.9 kcal/mol) and exhibits good stability. The residues Tyr-247 and Tyr-202, pivotal for binding in docking, were also confirmed via MD simulations. This study suggests that methyl indole-3-acetate holds potential applications in anti-inflammatory and anti-aging treatments.


Brevibacillus , Hyaluronoglucosaminidase , Molecular Docking Simulation , Molecular Dynamics Simulation , Hyaluronoglucosaminidase/antagonists & inhibitors , Hyaluronoglucosaminidase/metabolism , Brevibacillus/metabolism , Enzyme Inhibitors/pharmacology , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/metabolism , Hydrogen Bonding , Genome, Bacterial
4.
Int J Mol Sci ; 25(9)2024 Apr 26.
Article En | MEDLINE | ID: mdl-38731970

Malaria is a severe disease that presents a significant threat to human health. As resistance to current drugs continues to increase, there is an urgent need for new antimalarial medications. Aminoacyl-tRNA synthetases (aaRSs) represent promising targets for drug development. In this study, we identified Plasmodium falciparum tyrosyl-tRNA synthetase (PfTyrRS) as a potential target for antimalarial drug development through a comparative analysis of the amino acid sequences and three-dimensional structures of human and plasmodium TyrRS, with particular emphasis on differences in key amino acids at the aminoacylation site. A total of 2141 bioactive compounds were screened using a high-throughput thermal shift assay (TSA). Okanin, known as an inhibitor of LPS-induced TLR4 expression, exhibited potent inhibitory activity against PfTyrRS, while showing limited inhibition of human TyrRS. Furthermore, bio-layer interferometry (BLI) confirmed the high affinity of okanin for PfTyrRS. Molecular dynamics (MD) simulations highlighted the stable conformation of okanin within PfTyrRS and its sustained binding to the enzyme. A molecular docking analysis revealed that okanin binds to both the tyrosine and partial ATP binding sites of the enzyme, preventing substrate binding. In addition, the compound inhibited the production of Plasmodium falciparum in the blood stage and had little cytotoxicity. Thus, okanin is a promising lead compound for the treatment of malaria caused by P. falciparum.


Antimalarials , Molecular Docking Simulation , Molecular Dynamics Simulation , Plasmodium falciparum , Tyrosine-tRNA Ligase , Plasmodium falciparum/drug effects , Plasmodium falciparum/enzymology , Tyrosine-tRNA Ligase/antagonists & inhibitors , Tyrosine-tRNA Ligase/metabolism , Humans , Antimalarials/pharmacology , Antimalarials/chemistry , Enzyme Inhibitors/pharmacology , Enzyme Inhibitors/chemistry , Binding Sites , Protein Binding , Animals , Malaria, Falciparum/drug therapy , Malaria, Falciparum/parasitology
5.
Eur J Med Chem ; 271: 116443, 2024 May 05.
Article En | MEDLINE | ID: mdl-38691887

Xanthine oxidase (XO) is a key enzyme for the production of uric acid in the human body. XO inhibitors (XOIs) are clinically used for the treatment of hyperuricemia and gout, as they can effectively inhibit the production of uric acid. Previous studies indicated that both indole and isoxazole derivatives have good inhibitory effects against XO. Here, we designed and synthesized a novel series of N-5-(1H-indol-5-yl)isoxazole-3-carboxylic acids according to bioisosteric replacement and hybridization strategies. Among the obtained target compounds, compound 6c showed the best inhibitory activity against XO with an IC50 value of 0.13 µM, which was 22-fold higher than that of the classical antigout drug allopurinol (IC50 = 2.93 µM). Structure-activity relationship analysis indicated that the hydrophobic group on the nitrogen atom of the indole ring is essential for the inhibitory potencies of target compounds against XO. Enzyme kinetic studies proved that compound 6c acted as a mixed-type XOI. Molecular docking studies showed that the target compound 6c could not only retain the key interactions similar to febuxostat at the XO binding site but also generate some new interactions, such as two hydrogen bonds between the oxygen atom of the isoxazole ring and the amino acid residues Ser876 and Thr1010. These results indicated that 5-(1H-indol-5-yl)isoxazole-3-carboxylic acid might be an efficacious scaffold for designing novel XOIs and compound 6c has the potential to be used as a lead for further the development of novel anti-gout candidates.


Carboxylic Acids , Drug Design , Enzyme Inhibitors , Isoxazoles , Xanthine Oxidase , Xanthine Oxidase/antagonists & inhibitors , Xanthine Oxidase/metabolism , Structure-Activity Relationship , Enzyme Inhibitors/pharmacology , Enzyme Inhibitors/chemical synthesis , Enzyme Inhibitors/chemistry , Isoxazoles/chemistry , Isoxazoles/pharmacology , Isoxazoles/chemical synthesis , Carboxylic Acids/pharmacology , Carboxylic Acids/chemistry , Carboxylic Acids/chemical synthesis , Molecular Structure , Humans , Molecular Docking Simulation , Indoles/pharmacology , Indoles/chemistry , Indoles/chemical synthesis , Dose-Response Relationship, Drug
6.
J Cancer Res Clin Oncol ; 150(5): 253, 2024 May 15.
Article En | MEDLINE | ID: mdl-38748285

BACKGROUND: Lysine-specific demethylase 1 (LSD1) is highly expressed in a variety of malignant tumors, rendering it a crucial epigenetic target for anti-tumor therapy. Therefore, the inhibition of LSD1 activity has emerged as a promising innovative therapeutic approach for targeted cancer treatment. METHODS: In our study, we employed innovative structure-based drug design methods to meticulously select compounds from the ZINC15 database. Utilizing virtual docking, we evaluated docking scores and binding modes to identify potential inhibitors. To further validate our findings, we harnessed molecular dynamic simulations and conducted meticulous biochemical experiments to deeply analyze the binding interactions between the protein and compounds. RESULTS: Our results showcased that ZINC10039815 exhibits an exquisite binding mode with LSD1, fitting perfectly into the active pocket and forming robust interactions with multiple critical residues of the protein. CONCLUSIONS: With its significant inhibitory effect on LSD1 activity, ZINC10039815 emerges as a highly promising candidate for the development of novel LSD1 inhibitors.


Enzyme Inhibitors , Histone Demethylases , Molecular Docking Simulation , Histone Demethylases/antagonists & inhibitors , Histone Demethylases/metabolism , Histone Demethylases/chemistry , Humans , Enzyme Inhibitors/pharmacology , Enzyme Inhibitors/chemistry , Molecular Dynamics Simulation , Antineoplastic Agents/pharmacology , Antineoplastic Agents/chemistry , Drug Design , Neoplasms/drug therapy , Neoplasms/metabolism
7.
Eur J Med Chem ; 271: 116461, 2024 May 05.
Article En | MEDLINE | ID: mdl-38691891

Owing to the global health crisis of resistant pathogenic infections, researchers are emphasizing the importance of novel prevention and control strategies. Existing antimicrobial drugs predominantly target a few pathways, and their widespread use has pervasively increased drug resistance. Therefore, it is imperative to develop new antimicrobial drugs with novel targets and chemical structures. The de novo cysteine biosynthesis pathway, one of the microbial metabolic pathways, plays a crucial role in pathogenicity and drug resistance. This pathway notably differs from that in humans, thereby representing an unexplored target for developing antimicrobial drugs. Herein, we have presented an overview of cysteine biosynthesis pathways and their roles in the pathogenicity of various microorganisms. Additionally, we have investigated the structure and function of enzymes involved in these pathways as well as have discussed drug design strategies and structure-activity relationships of the enzyme inhibitors. This review provides valuable insights for developing novel antimicrobials and offers new avenues to combat drug resistance.


Cysteine , Drug Discovery , Cysteine/metabolism , Cysteine/chemistry , Cysteine/biosynthesis , Humans , Structure-Activity Relationship , Bacteria/drug effects , Bacteria/metabolism , Molecular Structure , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/chemistry , Anti-Bacterial Agents/biosynthesis , Enzyme Inhibitors/pharmacology , Enzyme Inhibitors/chemistry , Microbial Sensitivity Tests , Anti-Infective Agents/pharmacology , Anti-Infective Agents/chemistry , Anti-Infective Agents/metabolism
8.
Eur J Med Chem ; 271: 116437, 2024 May 05.
Article En | MEDLINE | ID: mdl-38701712

As a cytosolic enzyme involved in the purine salvage pathway metabolism, purine nucleoside phosphorylase (PNP) plays an important role in a variety of cellular functions but also in immune system, including cell growth, apoptosis and cancer development and progression. Based on its T-cell targeting profile, PNP is a potential target for the treatment of some malignant T-cell proliferative cancers including lymphoma and leukemia, and some specific immunological diseases. Numerous small-molecule PNP inhibitors have been developed so far. However, only Peldesine, Forodesine and Ulodesine have entered clinical trials and exhibited some potential for the treatment of T-cell leukemia and gout. The most recent direction in PNP inhibitor development has been focused on PNP small-molecule inhibitors with better potency, selectivity, and pharmacokinetic property. In this perspective, considering the structure, biological functions, and disease relevance of PNP, we highlight the recent research progress in PNP small-molecule inhibitor development and discuss prospective strategies for designing additional PNP therapeutic agents.


Enzyme Inhibitors , Purine-Nucleoside Phosphorylase , Small Molecule Libraries , Purine-Nucleoside Phosphorylase/antagonists & inhibitors , Purine-Nucleoside Phosphorylase/metabolism , Humans , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/pharmacology , Enzyme Inhibitors/chemical synthesis , Small Molecule Libraries/chemistry , Small Molecule Libraries/pharmacology , Molecular Structure , Animals , Antineoplastic Agents/pharmacology , Antineoplastic Agents/chemistry , Structure-Activity Relationship , Drug Development
9.
J Agric Food Chem ; 72(19): 10958-10969, 2024 May 15.
Article En | MEDLINE | ID: mdl-38703118

Demand for the exploration of botanical pesticides continues to increase due to the detrimental effects of synthetic chemicals on human health and the environment and the development of resistance by pests. Under the guidance of a bioactivity-guided approach and HSQC-based DeepSAT, 16 coumarin derivatives were discovered from the leaves of Ailanthus altissima (Mill.) Swingle, including seven undescribed monoterpenoid coumarins, three undescribed monoterpenoid phenylpropanoids, and two new coumarin derivatives. The structure and configurations of these compounds were established and validated via extensive spectroscopic analysis, acetonide analysis, and quantum chemical calculations. Biologically, 5 exhibited significant antifeedant activity toward the Plutella xylostella. Moreover, tyrosinase being closely related to the growth and development of larva, the inhibitory potentials of 5 against tyrosinase was evaluated in vitro and in silico. The bioactivity evaluation results highlight the prospect of 5 as a novel category of botanical insecticide.


Ailanthus , Coumarins , Insecticides , Plant Extracts , Plant Leaves , Plant Leaves/chemistry , Animals , Coumarins/pharmacology , Coumarins/chemistry , Ailanthus/chemistry , Plant Extracts/chemistry , Plant Extracts/pharmacology , Insecticides/chemistry , Insecticides/pharmacology , Molecular Structure , Larva/drug effects , Larva/growth & development , Moths/drug effects , Moths/growth & development , Monophenol Monooxygenase/antagonists & inhibitors , Monophenol Monooxygenase/metabolism , Biological Assay , Monoterpenes/pharmacology , Monoterpenes/chemistry , Feeding Behavior/drug effects , Enzyme Inhibitors/pharmacology , Enzyme Inhibitors/chemistry
10.
J Agric Food Chem ; 72(19): 10772-10780, 2024 May 15.
Article En | MEDLINE | ID: mdl-38703122

Protoporphyrinogen IX oxidase (PPO, E.C. 1.3.3.4) plays a pivotal role in chlorophyll biosynthesis in plants, making it a prime target for herbicide development. In this study, we conducted an investigation aimed at discovering PPO-inhibiting herbicides. Through this endeavor, we successfully identified a series of novel compounds based on the pyridazinone scaffold. Following structural optimization and biological assessment, compound 10ae, known as ethyl 3-((6-fluoro-5-(6-oxo-4-(trifluoromethyl)pyridazin-1(6H)-yl)benzo[d]thiazol-2-yl)thio)propanoate, emerged as a standout performer. It exhibited robust activity against Nicotiana tabacum PPO (NtPPO) with an inhibition constant (Ki) value of 0.0338 µM. Concurrently, we employed molecular simulations to obtain further insight into the binding mechanism with NtPPO. Additionally, another compound, namely, ethyl 2-((6-fluoro-5-(5-methyl-6-oxo-4-(trifluoromethyl)pyridazin-1(6H)-yl)benzo[d]thiazol-2-yl)thio)propanoate (10bh), demonstrated broad-spectrum and highly effective herbicidal properties against all six tested weeds (Leaf mustard, Chickweed, Chenopodium serotinum, Alopecurus aequalis, Poa annua, and Polypogon fugax) at the dosage of 150 g a.i./ha through postemergence application in a greenhouse. This work identified a novel lead compound (10bh) that showed good activity in vitro and excellent herbicidal activity in vivo and had promising prospects as a new PPO-inhibiting herbicide lead.


Drug Design , Enzyme Inhibitors , Herbicides , Nicotiana , Plant Proteins , Protoporphyrinogen Oxidase , Pyridazines , Protoporphyrinogen Oxidase/antagonists & inhibitors , Protoporphyrinogen Oxidase/metabolism , Protoporphyrinogen Oxidase/chemistry , Protoporphyrinogen Oxidase/genetics , Pyridazines/chemistry , Pyridazines/pharmacology , Herbicides/pharmacology , Herbicides/chemistry , Herbicides/chemical synthesis , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/pharmacology , Enzyme Inhibitors/chemical synthesis , Structure-Activity Relationship , Nicotiana/metabolism , Nicotiana/enzymology , Plant Proteins/chemistry , Plant Proteins/metabolism , Plant Proteins/antagonists & inhibitors , Plant Proteins/genetics , Molecular Docking Simulation , Molecular Structure , Plant Weeds/drug effects , Plant Weeds/enzymology , Kinetics
11.
J Agric Food Chem ; 72(19): 10794-10804, 2024 May 15.
Article En | MEDLINE | ID: mdl-38711396

Chitin-degrading enzymes are critical components in regulating the molting process of the Asian corn borer and serve as potential targets for controlling this destructive pest of maize. Here, we used a scaffold-hopping strategy to design a series of efficient naphthylimide insecticides. Among them, compound 8c exhibited potent inhibition of chitinase from OfChi-h and OfChtI at low nanomolar concentrations (IC50 = 1.51 and 9.21 nM, respectively). Molecular docking simulations suggested that 8c binds to chitinase by mimicking the interaction of chitin oligosaccharide substrates with chitinase. At low ppm concentrations, compound 8c performed comparably to commercial insecticides in controlling the highly destructive plant pest, the Asian corn borer. Tests on a wide range of nontarget organisms indicate that compound 8c has very low toxicity. In addition, the effect of inhibitor treatment on the expression of genes associated with the Asian corn borer chitin-degrading enzymes was further investigated by quantitative real-time polymerase chain reaction. In conclusion, our study highlights the potential of 8c as a novel chitinase-targeting insecticide for effective control of the Asian corn borer, providing a promising solution in the quest for sustainable pest management.


Chitin , Chitinases , Insect Proteins , Insecticides , Molecular Docking Simulation , Moths , Zea mays , Animals , Chitinases/chemistry , Chitinases/genetics , Chitinases/metabolism , Moths/enzymology , Moths/drug effects , Moths/genetics , Chitin/chemistry , Chitin/metabolism , Insecticides/chemistry , Insecticides/pharmacology , Insect Proteins/genetics , Insect Proteins/metabolism , Insect Proteins/chemistry , Insect Proteins/antagonists & inhibitors , Zea mays/chemistry , Zea mays/parasitology , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/pharmacology , Drug Design , Insect Control , Larva/growth & development , Larva/drug effects , Structure-Activity Relationship
12.
J Med Life ; 17(1): 87-98, 2024 Jan.
Article En | MEDLINE | ID: mdl-38737655

This study aimed to identify novel Glyoxalase-I (Glo-I) inhibitors with potential anticancer properties, focusing on anthraquinone amide-based derivatives. We synthesized a series of these derivatives and conducted in silico docking studies to predict their binding interactions with Glo-I. In vitro assessments were performed to evaluate the anti-Glo-I activity of the synthesized compounds. A comprehensive structure-activity relationship (SAR) analysis identified key features responsible for specific binding affinities of anthraquinone amide-based derivatives to Glo-I. Additionally, a 100 ns molecular dynamics simulation assessed the stability of the most potent compound compared to a co-crystallized ligand. Compound MQ3 demonstrated a remarkable inhibitory effect against Glo-I, with an IC50 concentration of 1.45 µM. The inhibitory potency of MQ3 may be attributed to the catechol ring, amide functional group, and anthraquinone moiety, collectively contributing to a strong binding affinity with Glo-I. Anthraquinone amide-based derivatives exhibit substantial potential as Glo-I inhibitors with prospective anticancer activity. The exceptional inhibitory efficacy of compound MQ3 indicates its potential as an effective anticancer agent. These findings underscore the significance of anthraquinone amide-based derivatives as a novel class of compounds for cancer therapy, supporting further research and advancements in targeting the Glo-I enzyme to combat cancer.


Amides , Anthraquinones , Enzyme Inhibitors , Lactoylglutathione Lyase , Molecular Docking Simulation , Anthraquinones/pharmacology , Anthraquinones/chemistry , Humans , Amides/chemistry , Amides/pharmacology , Lactoylglutathione Lyase/antagonists & inhibitors , Lactoylglutathione Lyase/metabolism , Enzyme Inhibitors/pharmacology , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/chemical synthesis , Structure-Activity Relationship , Molecular Dynamics Simulation , Antineoplastic Agents/pharmacology , Antineoplastic Agents/chemistry
13.
Molecules ; 29(9)2024 Apr 28.
Article En | MEDLINE | ID: mdl-38731521

Lactate dehydrogenase A (LDHA) primarily catalyzes the conversion between lactic acid and pyruvate, serving as a key enzyme in the aerobic glycolysis pathway of sugar in tumor cells. LDHA plays a crucial role in the occurrence, development, progression, invasion, metastasis, angiogenesis, and immune escape of tumors. Consequently, LDHA not only serves as a biomarker for tumor diagnosis and prognosis but also represents an ideal target for tumor therapy. Although LDHA inhibitors show great therapeutic potential, their development has proven to be challenging. In the development of LDHA inhibitors, the key active sites of LDHA are emphasized. Nevertheless, there is a relative lack of research on the amino acid residues around the active center of LDHA. Therefore, in this study, we investigated the amino acid residues around the active center of LDHA. Through structure comparison analysis, five key amino acid residues (Ala30, Met41, Lys131, Gln233, and Ala259) were identified. Subsequently, the effects of these five residues on the enzymatic properties of LDHA were investigated using site-directed mutagenesis. The results revealed that the catalytic activities of the five mutants varied to different degrees in both the reaction from lactic acid to pyruvate and pyruvate to lactic acid. Notably, the catalytic activities of LDHAM41G and LDHAK131I were improved, particularly in the case of LDHAK131I. The results of the molecular dynamics analysis of LDHAK131I explained the reasons for this phenomenon. Additionally, the optimum temperature of LDHAM41G and LDHAQ233M increased from 35 °C to 40 °C, whereas in the reverse reaction, the optimum temperature of LDHAM41G and LDHAK131I decreased from 70 °C to 60 °C. These findings indicate that Ala30, Met41, Lys131, Gln233, and Ala259 exert diverse effects on the catalytic activity and optimum temperature of LHDA. Therefore, these amino acid residues, in addition to the key catalytic site of the active center, play a crucial role. Considering these residues in the design and screening of LDHA inhibitors may lead to the development of more effective inhibitors.


Catalytic Domain , Enzyme Inhibitors , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/pharmacology , Humans , Amino Acids/chemistry , Amino Acids/metabolism , L-Lactate Dehydrogenase/antagonists & inhibitors , L-Lactate Dehydrogenase/metabolism , L-Lactate Dehydrogenase/chemistry , Lactate Dehydrogenase 5/metabolism , Lactate Dehydrogenase 5/antagonists & inhibitors , Lactate Dehydrogenase 5/chemistry , Pyruvic Acid/metabolism , Pyruvic Acid/chemistry , Mutagenesis, Site-Directed , Molecular Dynamics Simulation
14.
Molecules ; 29(9)2024 May 03.
Article En | MEDLINE | ID: mdl-38731613

Ribonuclease H (RNase H) was identified as an important target for HIV therapy. Currently, no RNase H inhibitors have reached clinical status. Herein, a series of novel thiazolone[3,2-a]pyrimidine-containing RNase H inhibitors were developed, based on the hit compound 10i, identified from screening our in-house compound library. Some of these derivatives exhibited low micromolar inhibitory activity. Among them, compound 12b was identified as the most potent inhibitor of RNase H (IC50 = 2.98 µM). The experiment of magnesium ion coordination was performed to verify that this ligand could coordinate with magnesium ions, indicating its binding ability to the catalytic site of RNase H. Docking studies revealed the main interactions of this ligand with RNase H. A quantitative structure activity relationship (QSAR) was also conducted to disclose several predictive mathematic models. A molecular dynamics simulation was also conducted to determine the stability of the complex. Taken together, thiazolone[3,2-a]pyrimidine can be regarded as a potential scaffold for the further development of RNase H inhibitors.


Anti-HIV Agents , Molecular Docking Simulation , Pyrimidines , Quantitative Structure-Activity Relationship , Pyrimidines/chemistry , Pyrimidines/pharmacology , Anti-HIV Agents/chemistry , Anti-HIV Agents/pharmacology , Anti-HIV Agents/chemical synthesis , Humans , Molecular Dynamics Simulation , Ribonuclease H/antagonists & inhibitors , Ribonuclease H/metabolism , Drug Design , HIV Infections/drug therapy , HIV-1/drug effects , HIV-1/enzymology , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/pharmacology , Thiazoles/chemistry , Thiazoles/pharmacology , Molecular Structure
15.
Nature ; 629(8011): 443-449, 2024 May.
Article En | MEDLINE | ID: mdl-38658754

The Werner syndrome RecQ helicase WRN was identified as a synthetic lethal target in cancer cells with microsatellite instability (MSI) by several genetic screens1-6. Despite advances in treatment with immune checkpoint inhibitors7-10, there is an unmet need in the treatment of MSI cancers11-14. Here we report the structural, biochemical, cellular and pharmacological characterization of the clinical-stage WRN helicase inhibitor HRO761, which was identified through an innovative hit-finding and lead-optimization strategy. HRO761 is a potent, selective, allosteric WRN inhibitor that binds at the interface of the D1 and D2 helicase domains, locking WRN in an inactive conformation. Pharmacological inhibition by HRO761 recapitulated the phenotype observed by WRN genetic suppression, leading to DNA damage and inhibition of tumour cell growth selectively in MSI cells in a p53-independent manner. Moreover, HRO761 led to WRN degradation in MSI cells but not in microsatellite-stable cells. Oral treatment with HRO761 resulted in dose-dependent in vivo DNA damage induction and tumour growth inhibition in MSI cell- and patient-derived xenograft models. These findings represent preclinical pharmacological validation of WRN as a therapeutic target in MSI cancers. A clinical trial with HRO761 (NCT05838768) is ongoing to assess the safety, tolerability and preliminary anti-tumour activity in patients with MSI colorectal cancer and other MSI solid tumours.


Antineoplastic Agents , Drug Discovery , Enzyme Inhibitors , Microsatellite Instability , Neoplasms , Synthetic Lethal Mutations , Werner Syndrome Helicase , Animals , Female , Humans , Mice , Administration, Oral , Allosteric Regulation/drug effects , Antineoplastic Agents/adverse effects , Antineoplastic Agents/chemistry , Antineoplastic Agents/pharmacology , Antineoplastic Agents/therapeutic use , Cell Line, Tumor , Clinical Trials as Topic , Colorectal Neoplasms/drug therapy , Colorectal Neoplasms/genetics , Colorectal Neoplasms/metabolism , Colorectal Neoplasms/pathology , DNA Damage/drug effects , Enzyme Inhibitors/adverse effects , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/pharmacology , Enzyme Inhibitors/therapeutic use , Mice, Nude , Neoplasms/drug therapy , Neoplasms/genetics , Neoplasms/pathology , Neoplasms/metabolism , Protein Domains , Reproducibility of Results , Suppression, Genetic , Synthetic Lethal Mutations/genetics , Tumor Suppressor Protein p53/metabolism , Tumor Suppressor Protein p53/genetics , Werner Syndrome Helicase/antagonists & inhibitors , Werner Syndrome Helicase/genetics , Werner Syndrome Helicase/metabolism , Xenograft Model Antitumor Assays
16.
mBio ; 15(5): e0063324, 2024 May 08.
Article En | MEDLINE | ID: mdl-38587428

Systemic infections by Candida spp. are associated with high mortality rates, partly due to limitations in current antifungals, highlighting the need for novel drugs and drug targets. The fungal phosphatidylserine synthase, Cho1, from Candida albicans is a logical antifungal drug target due to its importance in virulence, absence in the host, and conservation among fungal pathogens. Inhibitors of Cho1 could serve as lead compounds for drug development, so we developed a target-based screen for inhibitors of purified Cho1. This enzyme condenses serine and cytidyldiphosphate-diacylglycerol (CDP-DAG) into phosphatidylserine (PS) and releases cytidylmonophosphate (CMP). Accordingly, we developed an in vitro nucleotidase-coupled malachite-green-based high throughput assay for purified C. albicans Cho1 that monitors CMP production as a proxy for PS synthesis. Over 7,300 molecules curated from repurposing chemical libraries were interrogated in primary and dose-responsivity assays using this platform. The screen had a promising average Z' score of ~0.8, and seven compounds were identified that inhibit Cho1. Three of these, ebselen, LOC14, and CBR-5884, exhibited antifungal effects against C. albicans cells, with fungicidal inhibition by ebselen and fungistatic inhibition by LOC14 and CBR-5884. Only CBR-5884 showed evidence of disrupting in vivo Cho1 function by inducing phenotypes consistent with the cho1∆∆ mutant, including a reduction of cellular PS levels. Kinetics curves and computational docking indicate that CBR-5884 competes with serine for binding to Cho1 with a Ki of 1,550 ± 245.6 nM. Thus, this compound has the potential for development into an antifungal compound. IMPORTANCE: Fungal phosphatidylserine synthase (Cho1) is a logical antifungal target due to its crucial role in the virulence and viability of various fungal pathogens, and since it is absent in humans, drugs targeted at Cho1 are less likely to cause toxicity in patients. Using fungal Cho1 as a model, there have been two unsuccessful attempts to discover inhibitors for Cho1 homologs in whole-cell screens prior to this study. The compounds identified in these attempts do not act directly on the protein, resulting in the absence of known Cho1 inhibitors. The significance of our research is that we developed a high-throughput target-based assay and identified the first Cho1 inhibitor, CBR-5884, which acts both on the purified protein and its function in the cell. This molecule acts as a competitive inhibitor with a Ki value of 1,550 ± 245.6 nM and, thus, has the potential for development into a new class of antifungals targeting PS synthase.


Antifungal Agents , CDPdiacylglycerol-Serine O-Phosphatidyltransferase , Candida albicans , Enzyme Inhibitors , Candida albicans/drug effects , Candida albicans/enzymology , Candida albicans/genetics , Antifungal Agents/pharmacology , Antifungal Agents/chemistry , CDPdiacylglycerol-Serine O-Phosphatidyltransferase/genetics , CDPdiacylglycerol-Serine O-Phosphatidyltransferase/metabolism , CDPdiacylglycerol-Serine O-Phosphatidyltransferase/chemistry , Enzyme Inhibitors/pharmacology , Enzyme Inhibitors/chemistry , High-Throughput Screening Assays , Small Molecule Libraries/pharmacology , Small Molecule Libraries/chemistry , Microbial Sensitivity Tests , Fungal Proteins/genetics , Fungal Proteins/metabolism , Fungal Proteins/antagonists & inhibitors , Fungal Proteins/chemistry , Phosphatidylserines/metabolism , Furans , Thiophenes
17.
Int J Biol Macromol ; 267(Pt 1): 131407, 2024 May.
Article En | MEDLINE | ID: mdl-38582463

Succinate dehydrogenase (SDH) is an important inner mitochondrial membrane-bound enzyme involved in redox reactions during the tricarboxylic acid cycle. Therefore, a series of novel chitosan derivatives were designed and synthesized as potential microbicides targeting SDH and precisely characterized by FTIR, 1H NMR and SEM. Their antifungal and antibacterial activities were evaluated against Botrytis cinerea, Fusarium graminearum, Staphylococcus aureus and Escherichia coli. The bioassays revealed that these chitosan derivatives exerted significant antifungal effects, with four of the compounds achieving 100 % inhibition of Fusarium graminearum merely at a concentration of 0.5 mg/mL. Additionally, CSGDCH showed 79.34 % inhibition of Botrytis cinerea at a concentration of 0.1 mg/mL. In vitro antibacterial tests revealed that CSGDCH and CSGDBH have excellent Staphylococcus aureus and Escherichia coli inhibition with MICs of 0.0156 mg/mL and 0.03125 mg/mL, respectively. Molecular docking studies have been carried out to explore the binding energy and binding mode of chitosan and chitosan derivatives with SDH. The analyses indicated that chitosan derivatives targeted the active site of the SDH protein more precisely, disrupting its normal function and ultimately repressing the growth of microbial cells. Furthermore, the chitosan derivatives were also evaluated biologically for antioxidation, and all of these compounds had a greater degree of reducing power, superoxide radical, hydroxyl radical and DPPH-radical scavenging activity than chitosan. This research has the potential for the development of agricultural antimicrobial agents.


Antioxidants , Chitosan , Enzyme Inhibitors , Molecular Docking Simulation , Schiff Bases , Succinate Dehydrogenase , Chitosan/chemistry , Chitosan/pharmacology , Succinate Dehydrogenase/antagonists & inhibitors , Succinate Dehydrogenase/metabolism , Succinate Dehydrogenase/chemistry , Schiff Bases/chemistry , Schiff Bases/pharmacology , Schiff Bases/chemical synthesis , Antioxidants/pharmacology , Antioxidants/chemistry , Antioxidants/chemical synthesis , Enzyme Inhibitors/pharmacology , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/chemical synthesis , Glycine/chemistry , Glycine/analogs & derivatives , Glycine/pharmacology , Anti-Infective Agents/pharmacology , Anti-Infective Agents/chemistry , Anti-Infective Agents/chemical synthesis , Staphylococcus aureus/drug effects , Microbial Sensitivity Tests , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/chemistry , Anti-Bacterial Agents/chemical synthesis , Escherichia coli/drug effects , Antifungal Agents/pharmacology , Antifungal Agents/chemistry , Antifungal Agents/chemical synthesis , Fusarium/drug effects , Botrytis/drug effects , Chemistry Techniques, Synthetic
18.
Sci Rep ; 14(1): 9386, 2024 04 24.
Article En | MEDLINE | ID: mdl-38653790

Discovering effective anti-cancer agents poses a formidable challenge given the limited efficacy of current therapeutic modalities against various cancer types due to intrinsic resistance mechanisms. Cancer immunochemotherapy is an alternative strategy for breast cancer treatment and overcoming cancer resistance. Human Indoleamine 2,3-dioxygenase (hIDO1) and human Tryptophan 2,3-dioxygenase 2 (hTDO2) play pivotal roles in tryptophan metabolism, leading to the generation of kynurenine and other bioactive metabolites. This process facilitates the de novo synthesis of Nicotinamide Dinucleotide (NAD), promoting cancer resistance. This study identified a new dual hIDO1/hTDO2 inhibitor using a drug repurposing strategy of FDA-approved drugs. Herein, we delineate the development of a ligand-based pharmacophore model based on a training set of 12 compounds with reported hIDO1/hTDO2 inhibitory activity. We conducted a pharmacophore search followed by high-throughput virtual screening of 2568 FDA-approved drugs against both enzymes, resulting in ten hits, four of them with high potential of dual inhibitory activity. For further in silico and in vitro biological investigation, the anti-hypercholesterolemic drug Pitavastatin deemed the drug of choice in this study. Molecular dynamics (MD) simulations demonstrated that Pitavastatin forms stable complexes with both hIDO1 and hTDO2 receptors, providing a structural basis for its potential therapeutic efficacy. At nanomolar (nM) concentration, it exhibited remarkable in vitro enzyme inhibitory activity against both examined enzymes. Additionally, Pitavastatin demonstrated potent cytotoxic activity against BT-549, MCF-7, and HepG2 cell lines (IC50 = 16.82, 9.52, and 1.84 µM, respectively). Its anticancer activity was primarily due to the induction of G1/S phase arrest as discovered through cell cycle analysis of HepG2 cancer cells. Ultimately, treating HepG2 cancer cells with Pitavastatin affected significant activation of caspase-3 accompanied by down-regulation of cellular apoptotic biomarkers such as IDO, TDO, STAT3, P21, P27, IL-6, and AhR.


Antineoplastic Agents , Drug Repositioning , Indoleamine-Pyrrole 2,3,-Dioxygenase , Humans , Antineoplastic Agents/pharmacology , Antineoplastic Agents/chemistry , Indoleamine-Pyrrole 2,3,-Dioxygenase/antagonists & inhibitors , Indoleamine-Pyrrole 2,3,-Dioxygenase/metabolism , Tryptophan Oxygenase/antagonists & inhibitors , Tryptophan Oxygenase/metabolism , Cell Line, Tumor , Molecular Docking Simulation , Enzyme Inhibitors/pharmacology , Enzyme Inhibitors/chemistry , Drug Screening Assays, Antitumor , Apoptosis/drug effects , Cell Proliferation/drug effects , Pharmacophore
19.
Int J Mol Sci ; 25(8)2024 Apr 15.
Article En | MEDLINE | ID: mdl-38673942

Soluble epoxide hydrolase (sEH) is an enzyme targeted for the treatment of inflammation and cardiovascular diseases. Activated inflammatory cells produce nitric oxide (NO), which induces oxidative stress and exacerbates inflammation. We identify an inhibitor able to suppress sEH and thus NO production. Five flavonoids 1-5 isolated from Inula britannica flowers were evaluated for their abilities to inhibit sEH with IC50 values of 12.1 ± 0.1 to 62.8 ± 1.8 µM and for their effects on enzyme kinetics. A simulation study using computational chemistry was conducted as well. Furthermore, five inhibitors (1-5) were confirmed to suppress NO levels at 10 µM. The results showed that flavonoids 1-5 exhibited inhibitory activity in all tests, with compound 3 exhibiting the most significant efficacy. Thus, in the development of anti-inflammatory inhibitors, compound 3 is a promising natural candidate.


Epoxide Hydrolases , Flavonoids , Inula , Nitric Oxide , Epoxide Hydrolases/antagonists & inhibitors , Epoxide Hydrolases/metabolism , Animals , Nitric Oxide/metabolism , Mice , RAW 264.7 Cells , Flavonoids/pharmacology , Flavonoids/chemistry , Flavonoids/isolation & purification , Inula/chemistry , Enzyme Inhibitors/pharmacology , Enzyme Inhibitors/chemistry , Molecular Docking Simulation , Kinetics , Anti-Inflammatory Agents/pharmacology , Anti-Inflammatory Agents/chemistry , Flowers/chemistry
20.
BMC Complement Med Ther ; 24(1): 167, 2024 Apr 22.
Article En | MEDLINE | ID: mdl-38649994

Tanacetum falconeri is a significant flowering plant that possesses cytotoxic, insecticidal, antibacterial, and phytotoxic properties. Its chemodiversity and bioactivities, however, have not been thoroughly investigated. In this work, several extracts from various parts of T. falconeri were assessed for their chemical profile, antioxidant activity, and potential for enzyme inhibition. The total phenolic contents of T. falconeri varied from 40.28 ± 0.47 mg GAE/g to 11.92 ± 0.22 mg GAE/g in various extracts, while flavonoid contents were found highest in TFFM (36.79 ± 0.36 mg QE/g extract) and lowest (11.08 ± 0.22 mg QE/g extract) in TFSC (chloroform extract of stem) in similar pattern as found in total phenolic contents. Highest DPPH inhibition was observed for TFFC (49.58 ± 0.11 mg TE/g extract) and TFSM (46.33 ± 0.10 mg TE/g extract), whereas, TFSM was also potentially active against (98.95 ± 0.57 mg TE/g) ABTS radical. In addition, TFSM was also most active in metal reducing assays: CUPRAC (151.76 ± 1.59 mg TE/g extract) and FRAP (101.30 ± 0.32 mg TE/g extract). In phosphomolybdenum assay, the highest activity was found for TFFE (1.71 ± 0.03 mg TE/g extract), TFSM (1.64 ± 0.035 mg TE/g extract), TFSH (1.60 ± 0.033 mg TE/g extract) and TFFH (1.58 ± 0.08 mg TE/g extract), while highest metal chelating activity was recorded for TFSH (25.93 ± 0.79 mg EDTAE/g extract), TFSE (22.90 ± 1.12 mg EDTAE/g extract) and TFSC (19.31 ± 0.50 mg EDTAE/g extract). In biological screening, all extracts had stronger inhibitory capacity against AChE while in case of BChE the chloroform extract of flower (TFFC) and stem (TFSC) showed the highest activities with inhibitory values of 2.57 ± 0.24 and 2.10 ± 0.18 respectively. Similarly, TFFC and TFSC had stronger inhibitory capacity (1.09 ± 0.015 and 1.08 ± 0.002 mmol ACAE/g extract) against α-Amylase and (0.50 ± 0.02 and 0.55 ± 0.02 mmol ACAE/g extract) α-Glucosidase. UHPLC-MS study of methanolic extract revealed the presence of 133 components including sterols, triterpenes, flavonoids, alkaloids, and coumarins. The total phenolic contents were substantially linked with all antioxidant assays in multivariate analysis. These findings were validated by docking investigations, which revealed that the selected compounds exhibited high binding free energy with the enzymes tested. Finally, it was found that T. falconeri is a viable industrial crop with potential use in the production of functional goods and nutraceuticals.


Antioxidants , Plant Extracts , Tanacetum , Antioxidants/pharmacology , Antioxidants/chemistry , Plant Extracts/pharmacology , Plant Extracts/chemistry , Tanacetum/chemistry , Enzyme Inhibitors/pharmacology , Enzyme Inhibitors/chemistry , Flavonoids/pharmacology , Flavonoids/chemistry , Secondary Metabolism , Computer Simulation , Phenols/pharmacology , Phenols/chemistry
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