Molecular docking, pharmacokinetic studies, and in vivo pharmacological study of indole derivative 2-(5-methoxy-2-methyl-1H-indole-3-yl)-N'-[(E)-(3-nitrophenyl) methylidene] acetohydrazide as a promising chemoprotective agent against cisplatin induced organ damage

Indole-3-Lactic Acid Derived from Lacticaseibacillus paracasei Inhibits Helicobacter pylori Infection via Destruction of Bacteria Cells, Protection of Gastric Mucosa Epithelial Cells, and Alleviation of Inflammation

Indole-3-lactic acid (ILA) has exhibited antimicrobial properties. However, its role in inhibiting Helicobacter pylori infection remains elusive. This study investigated the inhibitory effect of ILA produced by Lacticaseibacillus paracasei on H. pylori, which was further confirmed by cell and animal experiments. 5 mg/mL ILA was sufficient to directly inhibit the growth of H. pylori in vitro, with a urease inhibitory activity reaching 60.94 ± 1.03%, and the cell morphology and structure were destroyed. ILA inhibited 56.5% adhesion of H. pylori to GES-1 and significantly reduced the number of apoptotic cells. Furthermore, ILA suppresses H. pylori colonization by approximately 38% to 63%, reduced inflammation and oxidative stress in H. pylori-infected mice, and enhanced the enrichment and variety of gut microbiota, notably fostering the growth of beneficial bacteria such as Lactobacillus and Bifidobacterium strains. The results support that ILA derived from Lactobacillus can be applicated as a novel prebiotic in anti-H. pylori functional foods.

Elucidation of Anti-Obesity Mechanisms of Phenolics in Artemisiae argyi Folium (Aiye) by Integrating LC-MS, Network Pharmacology, and Molecular Docking

The global prevalence of obesity is a pressing health issue, increasing the medical burden and posing significant health risks to humans. The side effects and complications associated with conventional medication and surgery have spurred the search for anti-obesity drugs from plant resources. Previous studies have suggested that Artemisiae argyi Folium (Aiye) water extracts could inhibit pancreatic lipase activities, control body weight increase, and improve the plasma lipids profile. However, the exact components and mechanisms were not precisely understood. Therefore, this research aims to identify the chemical profile of Aiye and provide a comprehensive prediction of its anti-obesity mechanisms. The water extract of Aiye was subjected to LC-MS analysis, which identified 30 phenolics. The anti-obesity mechanisms of these phenolics were then predicted, employing network pharmacology and molecular docking. Among the 30 phenolics, 21 passed the drug-likeness screening and exhibited 486 anti-obesity targets. The enrichment analysis revealed that these phenolics may combat obesity through PI3K-Akt signaling and MAPK, prolactin, and cAMP signaling pathways. Eight phenolics and seven central targets were selected for molecular docking, and 45 out of 56 docking had a binding affinity of less than -5 kcal/mol. This research has indicated the potential therapy targets and signaling pathways of Aiye in combating obesity.

Molecular modeling and simulation approaches to characterize potential molecular targets for burdock inulin to instigate protection against autoimmune diseases

In the current study, we utilized molecular modeling and simulation approaches to define putative potential molecular targets for Burdock Inulin, including inflammatory proteins such as iNOS, COX-2, TNF-alpha, IL-6, and IL-1β. Molecular docking results revealed potential interactions and good binding affinity for these targets; however, IL-1β, COX-2, and iNOS were identified as the best targets for Inulin. Molecular simulation-based stability assessment demonstrated that inulin could primarily target iNOS and may also supplementarily target COX-2 and IL-1β during DSS-induced colitis to reduce the role of these inflammatory mechanisms. Furthermore, residual flexibility, hydrogen bonding, and structural packing were reported with uniform trajectories, showing no significant perturbation throughout the simulation. The protein motions within the simulation trajectories were clustered using principal component analysis (PCA). The IL-1β-Inulin complex, approximately 70% of the total motion was attributed to the first three eigenvectors, while the remaining motion was contributed by the remaining eigenvectors. In contrast, for the COX2-Inulin complex, 75% of the total motion was attributed to the eigenvectors. Furthermore, in the iNOS-Inulin complex, the first three eigenvectors contributed to 60% of the total motion. Furthermore, the iNOS-Inulin complex contributed 60% to the total motion through the first three eigenvectors. To explore thermodynamically favorable changes upon mutation, motion mode analysis was carried out. The Free Energy Landscape (FEL) results demonstrated that the IL-1β-Inulin achieved a single conformation with the lowest energy, while COX2-Inulin and iNOS-Inulin exhibited two lowest-energy conformations each. IL-1β-Inulin and COX2-Inulin displayed total binding free energies of - 27.76 kcal/mol and - 37.78 kcal/mol, respectively, while iNOS-Inulin demonstrated the best binding free energy results at - 45.89 kcal/mol. This indicates a stronger pharmacological potential of iNOS than the other two complexes. Thus, further experiments are needed to use inulin to target iNOS and reduce DSS-induced colitis and other autoimmune diseases.

Human Intelectin-1 (hITL-1) as Modulator of Metabolic Syndrome (MetS): An In Silico Study

Human intelectin-1 (hITL-1) has been known to be involved in diseases such as asthma, cancer, metabolic disorders, and inflammatory bowel disease. In the present study, we aimed to evaluate hITL-1 as modulator of metabolic syndrome (MetS) using an in silico approach. AQ2 - The eight selected human (h) proteins, namely tumor necrosis factor-alpha (hTNF-alpha), myeloid differentiation primary response protein 88 (hMyD88), toll like-receptor 4 (hTLR4), cyclooxygenase 2 (hCOX 2), vascular cell adhesion molecule 1 (hVCAM 1), nuclear factor kappa B (hNF kappa B), leptin (hleptin), and interleukin 6 (hIL 6), were investigated on the docking analysis of hITL-1 (protein-protein) by using the HDOCK method. Furthermore, physicochemical properties of eight interested proteins were carried out using ProtParam tool. In the present study, two selected proteins, namely hMyD88, hCOX 2, have shown theoretical isoelectric point (PI) values greater than 7.0 which indicates these proteins are basic in nature. The protein-protein docking analysis showed that hNF kappa B exhibited the maximum docking score of -311.95 (kcal/mol) with the target protein hITL 1. Thus, the present find provides a new knowledge in understanding the hITL 1 as modulator of metabolic syndrome.

Blockade of phosphodiesterase 5 by sildenafil reduces tumor growth and potentiates tumor-killing ability of cisplatin in vivo against T cell lymphoma: Implication of modulated apoptosis, reactive oxygen species homeostasis, glucose metabolism, and pH regulation

In the past years, PDE5 has emerged as a promising therapeutic target for many cancers due to its highly upregulated expression. Interestingly, a recent in vitro study by our group has shown the antitumor and chemopotentiating action of sildenafil against T cell lymphoma. Our study showed that lower doses of sildenafil (50 μM) and cisplatin (0.5 μg/mL) exhibited 4% and 23% cytotoxicity against HuT78 cells, respectively, which was dramatically increased up to 50% when treated with both. Hence, the present study was designed to evaluate the antitumor and chemo-potentiating action of sildenafil in a murine model of T cell lymphoma (popularly called as Dalton's lymphoma [DL]). In the present study, DL-bearing mice were administered with vehicle (PBS), sildenafil (5 mg/kg bw), cisplatin (5 mg/kg bw), and sildenafil and cisplatin followed by evaluation of their impact on tumor growth by analyzing various parameters. The apoptosis was assessed by Wright-Giemsa, annexin-V, and DAPI staining. Reactive oxygen species (ROS) level was examined through DCFDA staining. The expression of genes and proteins were estimated by RT-PCR and Western blotting, respectively. The experimental findings of the study demonstrate for the first time that sildenafil inhibits tumor growth and potentiates tumor inhibitory ability of cisplatin by altering apoptosis, glycolysis, ROS homeostasis, and pH regulation in T cell lymphoma-carrying host. In addition, our investigation also showed amelioration of tumor-induced liver and kidney damage by sildenafil. Overall, the experimental data of our study strongly advocate the use and repurposing of SDF in designing promising chemotherapeutic regimens against malignancies of T cells.

Sciadopitysin mitigates spermatological and testicular damage instigated by paraquat administration in male albino rats

Paraquat (PQ) is a herbicide that has ability to induce testicular toxicity by producing reactive oxygen species (ROS). Sciadopitysin (SPS) is a promising flavonoid that displays multiple pharmacological properties i.e., anti-inflammatory, anti-oxidant and anti-apoptotic. Therefore, the present study was designed to evaluate the mitigative role of SPS against PQ induced testicular toxicity in male rats. The experiment was performed on male albino rats (n = 48) that were divided into 4 groups. The group-1 was control group. Group-2 was administrated orally with PQ (5 mg/kg). Group-3 was administrated orally with PQ (5 mg/kg) and SPS (2 mg/kg). Group-4 was supplemented with SPS (2 mg/kg) through oral gavage. The experiment was conducted for 56 days. The exposure to PQ significantly lowered the activities of catalase (CAT), glutathione reductase (GSR), superoxide dismutase (SOD) as well as glutathione peroxidase (GPx). Whereas, a substantial increase was observed in dead sperms number, abnormalities in the tail, head as well as midpiece of sperms in PQ intoxicated rats. Moreover, a significant increase in the level of ROS and malondialdehyde (MDA) was noticed in PQ administrated group. Furthermore, steroidogenic enzymes expression was significantly decreased in PQ-intoxicated group, whereas the level of inflammatory markers was increased in PQ administrated rats. Besides, the expression of apoptotic markers was significantly escalated in PQ exposed rats, whereas the expression of anti-apoptotic markers was considerably reduced. A significant reduction in hormonal level was also noticed in the rats that were administrated with PQ. Moreover, the histopathological examination revealed that PQ significantly damaged the testicles. However, the supplementation of SPS with PQ significantly reduced the adverse effects of PQ in the testes of albino rats. Therefore, the current investigation demonstrated that SPS possesses a significant potential to avert PQ-induced testicular dysfunction due to its anti-apoptotic, androgenic, anti-oxidant and anti-inflammatory nature.

The Chemosensing Role of CatSper in Mammalian Sperm: An Updated Review

After sperm enter the female reproductive tract, the physicochemical and biochemical microenvironment undergoes significant changes. In particular, the large changes in various ions encountered by sperm may alter the physiology of sperm, ultimately compromising capacitation and fertilization. Thus, the rapid response to environmental variations is vital for sperm functions. For example, Calcium, the most crucial ion for sperm functions, enters into sperm via Ca2+ permeable ion channels. The cation channel of sperm (CatSper) is a sperm-specific, pH-sensitive, and Ca2+-permeable ion channel. It is responsible for the predominant Ca2+ entry in mammalian sperm and is involved in nearly every event of sperm to acquire fertilizing capability. In addition, CatSper also serves as a pivotal polymodal chemosensor in mammalian sperm by responding to multiple chemical cues. Physiological chemicals (such as progesterone, prostaglandins, β-defensins, and odorants) provoke Ca2+ entry into sperm by activating CatSper and thus triggering sperm functions. Additionally, synthetic and natural chemicals (such as medicines, endocrine disrupting chemicals, drugs of abuse, and antioxidants) affect sperm functions by regulating CatSper-dependent Ca2+ signaling. Therefore, understanding the interactions between CatSper and extracellular ligands sheds light on the mechanisms underlying male infertility and offers innovative diagnostic and treatment approaches. This underscores the importance of CatSper as a crucial regulatory target in male reproduction, linking sperm function with the extracellular environment. In conclusion, this review comprehensively summarizes the relevant studies describing the environmental factors that affect CatSper in humans and rodents.

Abdellattif. Indenyl-thiazole and indenyl-formazan derivatives: Synthesis, anticancer screening studies, molecular-docking, and pharmacokinetic/ molin-spiration properties

Two new series of thiazole and formazan linked to 5-Bromo-indan were synthesized, and their structures were assured based on all possible analytical techniques. The size of the tested derivatives was calculated from the XRD technique and found five derivatives 3, 10a, 14a, 15, and 16 on the nanosized scale. The two series were tested for their efficacy and toxicity as anti-colon and stomach cancers. Derivative 10d showed activity more than the two reference drugs used in the case of SNU-16. Surpislly, in the case of COLO205, five derivatives 4, 6c, 6d, 6e, and 10a are better than the two benchmarks used, and two derivatives, 14a and 14b more potent than cisplatin. All potent derivatives showed a strong fit with the active site of the two tested proteins (gastric cancer (PDB = 2BID) and colon cancer (PDB = 2A4L)) in the molecular docking study. The Pharmacophore and ADME studies of the new derivatives showed that most derivatives revealed promising bioactivity, which indicates the drug-likeness properties against kinase inhibitors, protease, and enzyme inhibitors. In addition, the ProTox-II showed that the four compounds 10d, 16, 6d, and 10a are predicted to have oral LD50 values ranging from 335 to 3500 mg/kg in a rat model with (1 s,4 s)-Eucalyptol bearing the highest values and quercetin holding the lowest one.

In silico and in vitro anti-inflammatory study of phenolic compounds isolated from Eucalyptus maculata resin

Plant resins are rich in bioactive compounds with high medicinal values. However, the chemistry and anti-inflammatory activity of the resins produced by trees of the genus Eucalyptus were scarcely investigated. The inflammatory targets cyclooxygenase-1 (COX-1), COX-2, TNF-, NF-B, and NO were significantly inhibited by the methanolic extract of Eucalyptus maculata kino resin (EME) and its CH₂Cl₂ soluble fraction (MCF). Sakuranetin (C1), (E)-cinnamic acid (C2), kaempferol 7- methyl ether (C3), 7-O-methyl aromadendrin (C4), and 1,6- dicinnamoyl-O-α-D-glucopyranoside (C5) were isolated from MCF. Three compounds (C1, C2, and C4) showed potent in vitro COX-1 inhibition, while C5 inhibited COX-2, TNF-α, NF-κB, and NO significantly. An in-silico study revealed that C5 had the highest binding affinity to the active site in COX-2 with binding energy score (S) of -14.85 kcal/mol, better than celecoxib (COX-2 inhibitor). In conclusion, 1,6-dicinnamoyl-O-α-D-glucopyranoside (C5) could be investigated further in the search for anti-inflammatory agents.

Design, Synthesis, and Investigation of Cytotoxic Effects of 5-Hydroxyindole-3-Carboxylic Acid and Ester Derivatives as Potential Anti-breast Cancer Agents

Breast cancer is a deadly disease with a high prevalence rate among females. Despite several treatments, scientists are still engaged in finding less invasive treatments for this disease. The cellular proliferation rate and cell viability survey are critical to assess the drug's effect on both normal and malignant cell populations. Indole derivatives are promising candidates for their cytotoxic effect causing on breast cancer cells; however, they are less toxic on normal cells. This study synthesized 23 novel 5-hydroxyindole-3-carboxylic acids and related esters featuring various linear, cyclic, and primary aromatic amines. The MTT assay indicated the cytotoxicity of all acid and ester derivatives against the MCF-7 cells with no significant cytotoxicity on normal human dermal fibroblasts cells. Compound 5d, an ester derivative possessing a 4-methoxy group, was the most potent compound, with a half-maximal effective concentration of 4.7 µM. Compounds 5a, 5d, and 5l bearing ester group in their structure demonstrated cytotoxicity values < 10 µM against the MCF-7 cell line and were safe for advanced screening.

Prevention of Testicular Damage by Indole Derivative MMINA via Upregulated StAR and CatSper Channels with Coincident Suppression of Oxidative Stress and Inflammation: In Silico and In Vivo Validation

Cis-diamminedichloroplatinum (II) (CDDP) is a widely used antineoplastic agent with numerous associated side effects. We investigated the mechanisms of action of the indole derivative N'-(4-dimethylaminobenzylidene)-2-1-(4-(methylsulfinyl) benzylidene)-5-fluoro-2-methyl-1H-inden-3-yl) acetohydrazide (MMINA) to protect against CDDP-induced testicular damage. Five groups of rats (n = 7) were treated with saline, DMSO, CDDP, CDDP + MMINA, or MMINA. Reproductive hormones, antioxidant enzyme activity, histopathology, daily sperm production, and oxidative stress markers were examined. Western blot analysis was performed to access the expression of steroidogenic acute regulatory protein (StAR) and inflammatory biomarker expression in testis, while expression of calcium-dependent cation channel of sperm (CatSper) in epididymis was examined. The structural and dynamic molecular docking behavior of MMINA was analyzed using bioinformatics tools. The construction of molecular interactions was performed through KEGG, DAVID, and STRING databases. MMINA treatment reversed CDDP-induced nitric oxide (NO) and malondialdehyde (MDA) augmentation, while boosting the activity of glutathione peroxidase (GPx) and superoxide dismutase (SOD) in the epididymis and testicular tissues. CDDP treatment significantly lowered sperm count, sperm motility, and epididymis sperm count. Furthermore, CDDP reduced epithelial height and tubular diameter and increased luminal diameter with impaired spermatogenesis. MMINA rescued testicular damage caused by CDDP. MMINA rescued CDDP-induced reproductive dysfunctions by upregulating the expression of the CatSper protein, which plays an essential role in sperm motility, MMINA increased testosterone secretion and StAR protein expression. MMINA downregulated the expression of NF-κB, STAT-3, COX-2, and TNF-α. Hydrogen bonding and hydrophobic interactions were predicted between MMINA and 3β-HSD, CatSper, NF-κβ, and TNFα. Molecular interactome outcomes depicted the formation of one hydrogen bond and one hydrophobic interaction between 3β-HSD that contributed to its strong binding with MMINA. CatSper also made one hydrophobic interaction and one hydrogen bond with MMINA but with a lower binding affinity of -7.7 relative to 3β-HSD, whereas MMINA made one hydrogen bond with NF-κβ residue Lys37 and TNF-α reside His91 and two hydrogen bonds with Lys244 and Thr456 of STAT3. Our experimental and in silico results revealed that MMINA boosted the antioxidant defense mechanism, restored the levels of fertility hormones, and suppressed histomorphological alterations.

Cisplatin for cancer therapy and overcoming chemoresistance

Cisplatin spearheads the anticancer chemotherapeutics in present-day use although acute toxicity is its primary impediment factor. Among a plethora of experimental medications, a drug as effective or surpassing the benefits of cisplatin has not been discovered yet. Although Oxaliplatin is considered more superior to cisplatin, the former has been better for colorectal cancer while cisplatin is widely used for treating gynaecological cancers. Carcinoma imposes a heavy toll on mortality rates worldwide despite the novel treatment strategies and detection methods that have been introduced; nanomedicine combined with precision medicine, immunotherapy, volume-regulated anion channels, and fluorodeoxyglucose-positron emission tomography. Millions of deaths occur annually from metastatic cancers which escape early detection and the concomitant diseases caused by highly toxic chemotherapy that causes organ damage. It continues due to insufficient knowledge of the debilitative mechanisms induced by cancer biology. To overcome chemoresistance and to attenuate the adverse effects of cisplatin therapy, both in vitro and in vivo models of cisplatin-treated cancers and a few multi-centred, multi-phasic, randomized clinical trials in pursuant with recent novel strategies have been tested. They include plant-based phytochemical compounds, de novo drug delivery systems, biochemical/immune pathways, 2D and 3D cell culture models using small molecule inhibitors and genetic/epigenetic mechanisms, that have contributed to further the understanding of cisplatin's role in modulating the tumour microenvironment. Cisplatin was beneficial in cancer therapy for modulating the putative cellular mechanisms; apoptosis, autophagy, cell cycle arrest and gene therapy of micro RNAs. Specific importance of drug influx, efflux, systemic circulatory toxicity, half-maximal inhibition, and the augmentation of host immunometabolism have been identified. This review offers a discourse on the recent anti-neoplastic treatment strategies to enhance cisplatin efficacy and to overcome chemoresistance, given its superiority among other tolerable chemotherapies.

A Quantum Chemical Deep-Dive into the π-π Interactions of 3-Methylindole and Its Halogenated Derivatives—Towards an Improved Ligand Design and Tryptophan Stacking

Non-covalent π-π stacking interactions often play a key role in the stability of the secondary and tertiary structures of peptides and proteins, respectively, and can be a means of ensuring the binding of ligands within protein and enzyme binding sites. It is generally accepted that minor structural changes to the aromatic ring, such as substitution, can have a large influence on these interactions. Nevertheless, a thorough understanding of underpinning phenomena guiding these key interactions is still limited. This is especially true for larger aromatic structures. To expand upon this knowledge, elaborate ab initio calculations were performed to investigate the effect of halogenation on the stability of 3-methylindole stacking. 3-Methylindole served as a representation of the tryptophan side chain, and is a frequently used motif in drug design and development. Moreover, an expression is derived that is able to accurately predict the interaction stability of stacked halogenated 3-methylindole dimers as well as halogenated toluene dimers, based on monomer level calculated DFT descriptors. We aim for this expression to provide the field with a straightforward and reliable method to assess the effect of halogenation on the π-π stacking interactions between aromatic scaffolds.

Sulindac acetohydrazide derivative attenuates against cisplatin induced organ damage by modulation of antioxidant and inflammatory signaling pathways

This study aimed to explore the mechanisms of action of a sulindac acetohydrazide derivative, N'-(4-dimethylaminobenzylidene)-2-1-(4-(methylsulfinyl) benzylidene)-5-fluoro-2-methyl-1H-inden-3-yl) acetohydrazide, against anticancer drug cisplatin induced organ damage. Using a rodent model, various markers of organ function and signaling pathways were examined and validated by molecular docking studies. The study involves five groups of animals: control, DMSO, CDDP, CDDP + DMFM, and DMFM. Biochemical enzyme activity, histopathology, tissue antioxidant, and oxidative stress markers were examined. RT-PCR and western blot analyses were conducted for the expression of inducible cyclooxygenase enzyme (COX-2), nuclear factor kappa beta (NF-κB), p65, IL-1, TNF-α, and inducible nitric oxide synthase (iNOS). Flow cytometry analysis of CD4 + TNF-α, CD4 + COX-2, and CD4 + STAT-3 cells in whole blood was performed. Structural and dynamic behavior of DMFM upon binding with receptor molecule molecular docking and dynamic simulations were performed using bioinformatics tools and software. Treatment with DMFM reversed cisplatin-induced malondialdehyde (MDA) and nitric oxide (NO) induction, whereas the activity of glutathione peroxidase (GPx), and superoxide dismutase (SOD) in the kidney, heart, liver, and brain tissues were increased. DMFM administration normalized plasma levels of biochemical enzymes. We observed a marked decline in CD4 + STAT3, TNF-α, and COX2 cell populations in whole blood after treatment with DMFM. DMFM downregulated the expression factors related to inflammation at the mRNA and protein levels, i.e., IL-1, TNF-α, iNOS, NF-κB, STAT-3, and COX-2. Dynamic simulations and in silico docking data supports the experimental findings. Our experimental and in silico results illustrated that DMFM may affect protective action against cisplatin-induced brain, heart, liver, and kidney damage via reduction of inflammation and ROS.

Modular Representation of Physiologically Based Pharmacokinetic Models: Nanoparticle Delivery to Solid Tumors in Mice as an Example

Here we describe a toolkit for presenting physiologically based pharmacokinetic (PBPK) models in a modular graphical view in the BioUML platform. Firstly, we demonstrate the BioUML capabilities for PBPK modeling tested on an existing model of nanoparticles delivery to solid tumors in mice. Secondly, we provide guidance on the conversion of the PBPK model code from a text modeling language like Berkeley Madonna to a visual modular diagram in the BioUML. We give step-by-step explanations of the model transformation and demonstrate that simulation results from the original model are exactly the same as numerical results obtained for the transformed model. The main advantage of the proposed approach is its clarity and ease of perception. Additionally, the modular representation serves as a simplified and convenient base for in silico investigation of the model and reduces the risk of technical errors during its reuse and extension by concomitant biochemical processes. In summary, this article demonstrates that BioUML can be used as an alternative and robust tool for PBPK modeling.

Computational strategies to identify new drug candidates against neuroinflammation

The even more increasing application of computational approaches in these last decades has deeply modified the process of discovery and commercialization of new therapeutic entities. This is especially true in the field of neuroinflammation, in which both the peculiar anatomical localization and the presence of the blood-brain barrier makeit mandatory to finely tune the candidates' physicochemical properties from the early stages of the discovery pipeline. The aim of this review is therefore to provide a general overview to the readers about the topic of neuroinflammation, together with the most common computational strategies that can be exploited to discover and design small molecules controlling neuroinflammation, especially those based on the knowledge of the three-dimensional structure of the biological targets of therapeutic interest. The techniques used to describe the molecular recognition mechanisms, such as molecular docking and molecular dynamics, will therefore be eviscerated, highlighting their advantages and their limitations. Finally, we report several case studies in which computational methods have been applied in drug discovery on neuroinflammation, focusing on the last decade's research.