Biological Evaluation Research Articles

Discovery of novel natural-product-derived mutant isocitrate dehydrogenases 1 inhibitors: Structure-based virtual screening, biological evaluation and structure-activity relationship study

Mutations in IDH1 are commonly observed across various cancers, causing the conversion of α-KG to 2-HG. Elevated levels of 2-HG disrupt histone and DNA demethylation processes, promoting tumor development. Consequently, there is substantial interest in developing small molecule inhibitors targeting the mutant enzymes. Herein, we report a structure-based high-throughput virtual screening strategy using a natural products library, followed by hit-to-lead optimization. Through this process, we discover a potent compound, named 11s, which exhibited significant inhibition to IDH1 R132H and IDH1 R132C with IC50 values of 124.4 and 95.7 nM, respectively. Furthermore, 11s effectively reduced 2-HG formation, with EC50 values of 182 nM in U87 R132H cell, and 84 nM in HT-1080 cell. In addition, 11s significantly reduced U87 R132H and HT-1080 cell proliferation with GC50 values of 3.48 and 1.38 μM, respectively. PK-PD experiments further confirmed that compound 11s significantly decreased 2-HG formation in an HT-1080 xenograft mouse model, resulting in notable suppression of tumor growth without apparent loss in body weight.

Polymer Functionalization, Synthesis, Characterization, and Biological Evaluation of Silver Nanoparticles Using Cucurbita Maxima Leaf Extract

Polymer Functionalization, Synthesis, Characterization, and Biological Evaluation of Silver Nanoparticles Using Cucurbita Maxima Leaf Extract

3D printing of fish-scale derived hydroxyapatite/chitosan/PCL scaffold for bone tissue engineering

In the field of bone tissue repair, the treatment of bone defects has always posed a significant challenge. In recent years, the advancement of bone tissue engineering and regenerative medicine has sparked great interest in the development of innovative bone grafting materials. In this study, a novel hydroxyapatite (HA) material was successfully prepared and comprehensively characterized. Antimicrobial experiments and biological evaluations were conducted to determine its efficacy. Based on the aforementioned research findings, 3D printing technology was employed to fabricate HA/chitosan (CS)/ polycaprolactone (PCL) scaffolds. The composition of the scaffold materials was confirmed through X-ray diffractometer (XRD) and Fourier Transform Infrared Spectroscopy (FT-IR) tests, while the influence of different HA ratios on the scaffold surface morphology was observed. Additionally, antimicrobial experiments demonstrated the favorable antimicrobial activity of the scaffolds containing 30%HA + 5%CS + PCL. Furthermore, the water contact angle measurements confirmed the superhydrophilicity of the scaffolds. Finally, the excellent bioactivity and ability to promote tissue regeneration of the scaffolds were further confirmed by in vitro and in vivo experiments. This study provides new options for future repair and regeneration of bone tissue and clinical applications.

Design, synthesis, and biological evaluation of pyrido[2,3-d]pyrimidin-7(8H)-one derivatives as potent USP1 inhibitors

USP1 has emerged as a novel and potential target for drug discovery in single therapeutic agents or combination with chemotherapy and molecular targeted therapy. In this study, based on the disclosed structure of ML323 and KSQ-4279, we designed and synthesized a series of pyrido[2,3-d]pyrimidin-7(8H)-one derivatives as potent USP1 inhibitors by cyclization strategy and the systematic structure−activity relationship exploration was conducted. The representative compounds 1k, 1m and 2d displayed excellent USP1/UAF inhibition and exhibited strong antiproliferation effect in NCI–H1299 cells. Further flow cytometry analysis revealed that they could arrest breast cancer cells MDA-MB-436 in the S phase. Inhibition mechanism study of compound 1m indicated these derivatives acted as reversible and noncompetitive USP1 inhibitors. Of note, the combination of compound 1m with PARP inhibitor olaparib generated enhanced cell killing in olaparib-resistant MDA-MB-436/OP cells, and compound 1m exhibited excellent oral pharmacokinetic properties in mice. Overall, our efforts may provide a reliable basis for the development of novel USP1 inhibitor as a single therapeutic agent and in combination with PARP inhibitors.

Synthesis and biological evaluation of 2-(2-hydrazinyl) thiazole derivatives with potential antibacterial and antioxidant activity

Heterocyclic systems containing 2-(2-hydrazinyl) thiazole moieties were synthesized by heterocyclization of thiosemicarbazones with arylglyoxals and Meldrum's acid in ethanol and water 1:1 (v/v) under reflux conditions. The paper reports an efficient, facile, and environmentally friendly protocol via a novel one-pot three-component reaction to access a broad range of 2-(2-Hydrazinyl) thiazole derivatives. Products were isolated by plate chromatography and their structures were established from their spectroscopic data, then the antibacterial and antioxidant activity of synthesized 2-(2-hydrazinyl) thiazole derivatives were evaluated, and demonstrated encouraging antibacterial activity against Staphylococcus aureus as a gram positive bacteria and Escherichia coli as a gram negative bacteria. Furthermore, when representative products were assessed for radical scavenging activity against 2,2-diphenyl-1-picrylhydrazyl (DPPH0), high antioxidant effects were observed, indicating their potential safety for use in pharmacological studies.

Synthesis of 2-Aryl Indazole: Synthesis, Biological Evaluationand In-Silico Studies.

In this work, a highly effective synthesis technique for obtaining aryl indazole under mild circumstances is provided, using trimethyl phosphine as a powerful reagent. The procedure shows that a wide range of substrates can be investigated, yielding various 2-aryl indazole derivatives with acceptable to exceptional yields and a wide range of functional group tolerance. Additionally, based on In Silico studies tests were conducted to determine the anticancer activity In Vitro for all produced compounds (3 a-3 j) against A549, HT-29 and HepG2 cell lines. Compounds 3 c and 3 d, with IC50 values of 15, 53.55, 7.34, 7.10, 56.28, and 17.87 (μM) against A549, HT-29 and HepG2 respectively, showed significant anticancer activity.

Synthesis, biological evaluation, and computational studies of thiazolyl hydrazone derivatives as triple mutant allosteric EGFR inhibitors

AbstractHerein, new thiazole‐2‐yl‐based hydrazone derivatives were synthesized and assessed for in vitro anticancer activity against wild type A549, MCF7, DU145, and mutant H1975 cancer cell lines by 3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyltetrazolium bromide (MTT) assay. Among all, 4‐(4‐Chlorophenyl)‐2‐(2‐((4‐methylthiazol‐5‐yl)methylene)hydrazineyl)thiazole (4b) elicited prominent anticancer activity against wild‐type epidermal growth factor receptor (WT‐EGFR) MCF7 cancer cell line with an IC50 value of 9.57 ± 1.80 μM, whereas 4‐Methyl‐5‐((2‐(4‐(4‐nitrophenyl)thiazol‐2‐yl)hydrazineylidene)methyl)thiazole (4c) showed appreciable activity with an IC50 value of 11 ± 0.7 μM against the mutated EGFR H1975 lung cancer cells. Doxorubicin and Osimertinib were used as the standard drugs for comparison of activity. Compound (4b) significantly increased early apoptosis (30.2%) and late apoptosis (7.6%) at a 5 μM concentration in comparison with the control (early apoptosis 2.5%, late apoptosis 1.2%). The molecular docking study was performed against mutant EGFR (T790M/C797S) (PDB: 5D41) enzyme to gain information about interactions of synthesized molecules with binding pockets. Moreover, ADME study and molecular dynamic simulation studies were accomplished to gain insight into drug‐likeness and conformational stability, respectively. The findings demonstrate a promising alignment between the observed anticancer effects and computational analyses.

Discovery of novel CDK9 inhibitor with tridentate ligand: Design, synthesis and biological evaluation

Cyclin-dependent kinase 9 (CDK9) plays a role in transcriptional regulation, which had become an attractive target for discovery of antitumor agent. In this work, beyond traditional CDK9 inhibitor with bidentate ligands in ATP binding domain, a series of novel CDK9 inhibitor with tridentate ligand were designed and synthesized. Surprisingly, this unique tridentate ligand structure endows better CDK9 inhibition selectivity compared to other CDK subtypes, and the lead candidate compound Z4-7a showed effective proliferation inhibition in HCT116 cells with acceptable pharmacokinetic properties. Research on the mechanism indicated that Z4-7a could induce apoptosis in the HCT116 cell line by inhibiting phosphorylation of RNA polymerase II at Ser2, which resulted in the inhibition of apoptosis-related genes and proteins expression. In brief, introduction of tridentate ligand might work as a promising strategy for the development of novel selective CDK9 inhibitor.

Design, Synthesis, and Biological Evaluation of New Type of Gemini Analogues with a Cyclopropane Moiety in Their Side Chain.

We synthesized two new gemini analogues, UG-480 and UG-481, that incorporate a modified longer side chain containing a cyclopropane group. The evaluation of the bioactivities of the two gemini analogues indicated that the 17,20 threo (20S) compound, UG-480, is the most active one and is as active as 1,25(OH)2D3. Docking and molecular dynamics (MD) data showed that the compounds bind efficiently to vitamin D receptor (VDR) with UG-480 to form an energetically more favorable interaction with His397. Structural analysis indicated that whereas the UG-480 compound efficiently stabilizes the active VDR conformation, it induces conformational changes in the H6-H7 VDR region that are greater than those induced by the parental Gemini and that this is due to the occupancy of the secondary channel by its modified side chain.

Synthesis, biological evaluation and in silico molecular modelling studies of chloro substituted bis-indole containing benzohydrazide analogues as potential anti-diabetic and anti-Alzheimer's agents

Fifteen bis-indolylmethane analogues were synthesized, characterized through NMR (1H, 13C) and high-resolution electron-impact mass spectrometry (HREI-MS), and tested against α-glucosidase, α-amylase, acetylcholinesterase, and butyrylcholinesterase inhibitory potentials. All analogues exhibited different inhibitory potentials, with IC50 values ranging between 7.5 ± 0.92 to 58.4 ± 0.07 μM (α-glucosidase), and 0.80 ± 0.05 to 15.30 ± 0.10 μM (α-amylase) as compared to the standard drug acarbose (IC50 = 38.45 ± 0.80 and 8.90 ± 0.10 μM). Out of fifteen analogues, nine showed an excellent inhibitory potency that was manyfold better than standard drugs. A slight increase or decrease in inhibition was observed due to substituents attached at imine site. In the case of α-amylase inhibition, two analogues such as 2 and 11, showed excellent inhibitory potential with IC50 values of 0.80 ± 0.05 and 0.90 ± 0.10 μM while all other analogues showed good potency. All analogues were also tested against acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) inhibitory potentials, and they showed good potentials ranging from 1.40 ± 0.20 to 16.20 ± 0.50 μM (AChE) and 3.20 ± 0.10 to 19.60 ± 0.20 μM (BuChE) as compared to the standard drug Donepezil (IC50 = 2.16 ± 0.12 μM and 4.5 ± 0.11 μM). In the case of AChE, analogue 3 is the most potent, and in the case of BuChE, analogue 9 is the most potent among the series. The structure-activity relationship was carried out, mainly associated with the nature, number, and position and the electron-donating and electron-withdrawing effects of the substituent(s) on the phenyl ring. The binding modes as well as binding free energy for α-glucosidase and α-amylase inhibitors were determined through docking studies.

Synthesis, molecular modeling simulations and anticancer activity of some new Imidazo[2,1-b]thiazole analogues as EGFR/HER2 and DHFR inhibitors

New imidazo[2,1-b]thiazole analogs were designed, synthesized, and biologically evaluated as anticancer agents. In vitro biological evaluation of the anticancer properties of the compounds was performed against different cancer cell lines. Compounds 23 and 39 showed remarkable broad −spectrum cytotoxic potency on most of the tested cell lines. Compounds 23 and 39 exhibited potent activity against the MCF-7 breast cancer cell line, with IC50 values of 1.81 and 4.95 μM, respectively, compared to DOX and SOR (IC50 values of 4.17 and 7.26 μM, respectively). An enzyme inhibition assay was carried out to clarify the possible mode of action of the tested compounds. Compounds 23 and 39 were identified as possible EGFR, HER-2, and DHFR inhibitors. Cell cycle arrest results indicated that compound 23 caused cell cycle arrest at the G0/G1 phase in the MCF-7 cells and at the G2/M phase in the Hep G2 cells. Compound 39 induced cell cycle arrest at the G2/M phase in Hela cells. In vivo testing of the anticancer activity of the two most promising molecules in this study was conducted, and the results indicated that they possess considerable in vivo anticancer activity in mice. Data obtained from the molecular modeling simulation study were consistent with the biological evaluation results.

Synthesis and biological evaluation of panaxadiol ester derivatives possessing pyrazole and pyrrole moiety as HIF-1α inibitors

Hypoxia-inducing factor-1α (HIF-1α) is overexpressed in variety of tumor patients and plays an important role in the regulation of hypoxia response in tumor cells. Therefore, its inhibitors have become one of the targets for the treatment of a variety of cancers. Two series of panaxadiol (PD) ester derivatives containing pyrazole (18a–j) and pyrrole (19a–n) moiety were synthesized and their HIF-1α inhibitory activities were evaluated. Among all the target compouds, compounds 18c, 19d, and 19n (IC50 = 8.70–10.44 μM) showed better HIF-1α inhibitory activity than PD (IC50 = 13.35 μM). None of these compounds showed cytotoxicity above 100 μM and inhibited HIF-1α transcription in a dose-dependent manner. These compounds showed good antitumor activity and provide lead compounds for further design and activity study of PD ester derivatives.

Stereospecific Synthesis and Biological Evaluation of KRN7000 Analogues with Thio-modifications at the Acyl Moiety.

α-Galactosylceramide (KRN7000 or α-GalCer) analogues terminated with phenyl (Ph) groups at the acyl moiety possess more potency than KRN7000 to activate invariant natural killer T (iNKT) cells for inducing a T helper 1 (Th1)-biased immune response. However, biological activities of phenyl glycolipids with thio-modifications at the acyl moiety remain unknown, and facile approaches for highly stereoselective synthesis of KRN7000 and its analogues are rather scarce. Herein, we exploited 4,6-di-O-tert-butylsilylene (DTBS)-directed stereospecific galactosylation to efficiently synthesize various α-GalCer analogues bearing thioamide, terminal thiophenyl and dual modifications at the acyl moiety. Biological evaluations suggest that a new analogue S34 featuring a terminal Ph-S-Ph-F group exhibits a more superior Th1-biased immune response in mice. Molecular docking analysis revealed that the introduction of a sulfur atom influences vital hydrogen bonding interactions between glycolipids and the cluster of differentiation 1d (CDld), thus adjusting the stability of the glycolipid-CDld complex.

Synthesis and Biological Evaluation of Fluorine-18 and Deuterium Labeled l-Fluoroalanines as Positron Emission Tomography Imaging Agents for Cancer Detection.

To fully explore the potential of 18F-labeled l-fluoroalanine for imaging cancer and other chronic diseases, a simple and mild radiosynthesis method has been established to produce optically pure l-3-[18F]fluoroalanine (l-[18F]FAla), using a serine-derivatized, five-membered-ring sulfamidate as the radiofluorination precursor. A deuterated analogue, l-3-[18F]fluoroalanine-d3 (l-[18F]FAla-d3), was also prepared to improve metabolic stability. Both l-[18F]FAla and l-[18F]FAla-d3 were rapidly taken up by 9L/lacZ, MIA PaCa-2, and U87MG cells and were shown to be substrates for the alanine-serine-cysteine (ASC) amino acid transporter. The ability of l-[18F]FAla, l-[18F]FAla-d3, and the d-enantiomer, d-[18F]FAla-d3, to image tumors was evaluated in U87MG tumor-bearing mice. Despite the significant bone uptake was observed for both l-[18F]FAla and l-[18F]FAla-d3, the latter had enhanced tumor uptake compared to l-[18F]FAla, and d-[18F]FAla-d3 was not specifically taken up by the tumors. The enhanced tumor uptake of l-[18F]FAla-d3 compared with its nondeuterated counterpart, l-[18F]FAla, warranted the further biological investigation of this radiotracer as a potential cancer imaging agent.

X‐ray crystallographic of a novel pyrimidine ligand (LPH) and its metal chelates Cr3+, Ni2+, and Ru3+: A comprehensive study on synthesis, characterization, computational investigations, and biological evaluation toward anticancer and antioxidant

2,4,6‐Triamino‐N‐phenylpyrimidine‐5‐carbothioamide (LPH) was synthesized and extensively characterized. Single crystal X‐ray confirms a monoclinic P21/c space group for LPH. The novel ligand and its chelates of Cr3+, Ni2+, and Ru3+ were studied by elemental analyses, spectral (13C‐,1H‐NMR, UV–visible, IR), magnetic, and thermal measurements. IR spectra indicated that LPH behaves in a bidentate mode through the two NH2 groups of the pyrimidine ring and/or a tetradentate coordination involving the nitrogen atoms of the two NH2 of the pyrimidine ring, NH, and the thioketo (C=S) groups, respectively. By utilizing the Gaussian 09 W program in DFT/B3LYP, we are able to conduct computational estimates of LPH and its metal chelates, yielding insightful data regarding their electronic structure and stability. Biological studies were conducted to assess the isolated compounds' activities against anticancer (MCF‐7), antioxidant (DPPH and ABTS), DNA, and antimicrobial proteins. Molecular docking was employed to investigate the chelates' inhibitory properties, specifically their binding propensity with MCF‐7 cells, revealing possible anticancer action. All the data help to understand LPH and its complexes' production, biological characteristics, and possible therapeutic uses.

New insights into aflatoxin B1 mechanistic toxicology in cattle liver: an integrated approach using molecular docking and biological evaluation in CYP1A1 and CYP3A74 knockout BFH12 cell lines.

Aflatoxin B1 (AFB1) is a pro-carcinogenic compound bioactivated in the liver by cytochromes P450 (CYPs). In mammals, CYP1A and CYP3A are responsible for AFB1 metabolism, with the formation of the genotoxic carcinogens AFB1-8,9-epoxide and AFM1, and the detoxified metabolite AFQ1. Due to climate change, AFB1 cereals contamination arose in Europe. Thus, cattle, as other farm animals fed with grains (pig, sheep and broiler), are more likely exposed to AFB1 via feed with consequent release of AFM1 in milk, posing a great concern to human health. However, knowledge about bovine CYPs involved in AFB1 metabolism is still scanty. Therefore, CYP1A1- and CYP3A74-mediated molecular mechanisms of AFB1 hepatotoxicity were here dissected. Molecular docking of AFB1 into CYP1A1 model suggested AFB1 8,9-endo- and 8,9-exo-epoxide, and AFM1 formation, while docking of AFB1 into CYP3A74 pointed to AFB1 8,9-exo-epoxide and AFQ1 synthesis. To biologically confirm these predictions, CYP1A1 and CYP3A74 knockout (KO) BFH12 cell lines were exposed to AFB1. LC-MS/MS investigations showed the abolished production of AFM1 in CYP1A1 KO cells and the strong increase of parent AFB1 in CYP3A74 KO cells; the latter result, coupled to a decreased cytotoxicity, suggested the major role of CYP3A74 in AFB1 8,9-exo-epoxide formation. Finally, RNA-sequencing analysis indirectly proved lower AFB1-induced cytotoxic effects in engineered cells versus naïve ones. Overall, this study broadens the knowledge on AFB1 metabolism and hepatotoxicity in cattle, and it provides the weight of evidence that CYP1A1 and CYP3A74 inhibition might be exploited to reduce AFM1 and AFBO synthesis, AFB1 toxicity, and AFM1 milk excretion.

Discovery of a novel DYRK1A inhibitor with neuroprotective activity by virtual screening and in vitro biological evaluation.

Dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A) is implicated in accumulation of amyloid β-protein (Aβ) and phosphorylation of Tau proteins, and thus represents an important therapeutic target for neurodegenerative diseases. Though many DYRK1A inhibitors have been discovered, there is still no marketed drug targeting DYRK1A. This is partly due to the lack of effective and safe chemotypes. Therefore, it is still necessary to identify new classes of DYRK1A inhibitors. By performing virtual screening with the workflow mainly composed of pharmacophore modeling and molecular docking as well as the following DYRK1A inhibition assay, we identified compound L9, ((Z)-1-(((5-phenyl-1H-pyrazol-4-yl)methylene)-amino)-1H-tetrazol-5-amine), as a moderately active DYRK1A inhibitor (IC50: 1.67μM). This compound was structurally different from the known DYRK1A inhibitors, showed a unique binding mode to DYRK1A. Furthermore, compound L9 showed neuroprotective activity against okadaic acid (OA)-induced injury in the human neuroblastoma cell line SH-SY5Y by regulating the expression of Aβ and phosphorylation of Tau protein. This compound was neither toxic to the SH-SY5Y cells nor to the human normal liver cell line HL-7702 (IC50: >100μM). In conclusion, we have identified a novel DYRK1A inhibitor with neuroprotective activity through virtual screening and in vitro biological evaluation, which holds the promise for further study.

Synthesis and Biological Evaluation of a Series of New Hybrid Amide Derivatives of Triazole and Thiazolidine-2,4-dione.

A series of hybrid compounds with triazole and thiazolidine nuclei connected by a linker has been synthesized and extensively studied. Various synthetic methods for the target compounds have been tested. A microbiological assessment of the obtained compounds was carried out on strains of pathogenic fungi C. albicans, C. non-albicans, multidrug-resistant C. auris, Rhizopus arrhizus, Aspergillus spp. and some dermatophytes and other yeasts. The lowest obtained MIC values for target compounds lie between 0.003 µg/mL and 0.5 µg/mL and therefore the compounds are not inferior or several times better than commercial azole drugs. The length of the acylpiperazine linker has a limited effect on antifungal activity. Some bioisosteric analogues were tested in microbiological analysis, but turned out to be weaker than the leader in activity. The highest activity was demonstrated by a compound with para-chlorobenzylidene substituent in the thiazolidine fragment. Molecular modelling was used to predict binding modes of synthesized molecules and rationalize experimentally observed SAR. The leader compound is twice more effective in inhibiting the formation of germ tubes by Candida albicans yeast cells compared to voriconazole. An increased level of Pdr5, an azoles drug efflux pump was observed, but the increase is lower than that caused by azoles. The results can be useful for further development of more powerful and safe antifungal agents.

Polymorphic strategies for encapsulating polyindole@nido-carborane fluorescent polymeric nanocapsules: Their release, imaging, and biological evaluation in the gastrointestinal microenvironment

In this experiment, by combining water-soluble nido-carborane with indole dyes, and used non-toxic and non-irritating sodium alginate and acrylic resin as coating materials to obtain four fluorescent complexes, indol-nido-carborane-sodium alginate- Polymer-A (INS-A) 、indol-nido-carborane-sodium alginate-Polymer-B (INS-B)、indol-nido-carborane-sodium alginate-Polymer-C (INS-C) and indol-nido-carborane-sodium alginate-Polymer-D (INS-D).The transmission electron microscopy (TEM) results showed that the four complexes have different morphologies, with INS-A showing irregular clusters, INS-B being uniformly spherical, INS-C demonstrating a cashew-nut shape and INS-D manifesting a semi-encapsulated state. The spectroscopic properties and in vitro release experiments of the four complexes were performed in different simulated gastrointestinal environments. The results indicated that INS-A and INS-C had excellent photophysical properties and high cumulative release, so INS-A and INS-C were selected for subsequent experiments. Atomic Force Microscope (AFM) test manifested that the surfaces of INS-A and INS-C were relatively smooth. Imaging of HeLa cells with different channels was performed, the Pearson correlation coefficients of both INS-A and INS-C could be calculated to be distributed between 0.21 and 0.60, indicating that the complexes exhibited good imaging performance and could enter the cell and distribute around the nucleus. The results of cell proliferation toxicity (CCK8) experiments showed that at the concentration of 125 μg/mL, the inhibition rates of INS-A and INS-C on HCT-116 and HeLa cells were 47.15 %, 36.70 % and 42.81 %, 35.52 %, respectively, demonstrating that the complexes had an inhibitory effect on cancer cells. In summary, the fluorescent complexes prepared in this paper have good imaging ability and tumor targeting, and are potential fluorescent anticancer reagent.

Emodin Alcohols: Design, Synthesis, Biological Evaluation and Multitargeting Studies with DNA, RNA, and HSA.

A series of novel emodin alcohols were designed and prepared in an effort to overcome the increasing microorganism resistance. Novel emodin alcohols were prepared from commercial emodin and different nitrogen-containing heterocycles via different synthetic strategies, such as O-alkylation and N-alkylation. The antimicrobial activity of synthesized emodin compounds was evaluated in vitro by a two-fold serial dilution technique. The interaction of emodin compound 3d with biomolecule was researched using UV-vis spectroscopic method and fluorescence spectroscopy. Emodin compound 3d containing 2-methyl-5-nitro imidazole ring showed relatively good antimicrobial activity. Notably, it exhibited equivalent activity against S. aureus in comparison to the reference drug norfloxacin (MIC = 4 μg/mL). The combination of strong active compound 3d with reference drugs showed better antimicrobial activity with less dosage and a broader antimicrobial spectrum than their separate use. Further research displayed that emodin compound 3d could intercalate into S. aureus DNA to form the 3d-DNA complex, which might correlate with the inhibitory activity. The hydrogen bonds were found between S. aureus DNA gyrase and strong active compound 3d during the docking research, which were in accordance with the spectral experiment results. The interaction with yeast RNA of compound 3d could also form a complex via hydrogen bonds. The hydrogen bonds were found to play a major role in the transportation of emodin compound 3d by human serum albumin (HSA), as confirmed by molecular simulation. This work provides a promising starting point to optimize the structures of emodin derivatives as potent antimicrobial agents.