Letters in Drug Design & Discovery - Volume 21, Issue 13, 2024

Charcot Marie Tooth Disease-2 is a debilitating neurogenetic disorder that adversely affects peripheral neurons by disrupting mitochondrial activity. Mutated mitofusin-2 (MFN) is the main culprit behind disruptive mitochondrial function and is considered a therapeutic target in identifying drugs for treating this disease. This disease has no therapeutic medication except for supportive care.

The objective of the current study is to evaluate high-affinity medicinal compounds for mutated MFN-2 and describe their absorption, distribution, metabolism, excretion, and toxic attributes (ADMET).

For ADMET properties, 2,219 medicinal compounds were analyzed with AutoDock Vina using PyRX 0.9 software against MFN-2, SwissADME, and GUSAR.

Results from screening studies revealed that three compounds (Liriodenine, Pinocembrin, and Vestitol) show an affinity for amino acids present in the predicted active interface of the MFN-2 protein. Moreover, these compounds render low toxicity and efficient ADME qualities, combined with blood-brain barrier permeability, drug-likeness, and lead-likeness.

Liriodenine, pinocembrin and vestitol are therapeutic compounds for CMT-2 treatment and should be used in further in vitro studies to confirm the results of this research.

Novel antibiotics are needed to stem the rise of antimicrobial resistance. N-Methyl-2-phenylmaleimide (NMP) compounds previously synthesised by our research group are structural analogues of 2,3,5-substituted perhydropyrrolo[3,4-d]isoxazole-4,6-diones found by others to have antibacterial activity.

This study aims to explain the significance of NMPs and their antibacterial activity. The antibacterial activity of the NMPs was determined against Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa. The partition coefficient of the NMPs and a pharmacophore model were used to explain their antibacterial activity.

The Kirby Bauer Disc diffusion method was used to screen the NMPs for activity, while the broth microdilution method was used to determine the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of the active NMPs. Using the in vitro antibacterial activity of 2,3,5-substituted perhydropyrrolo[3,4-d]isoxazole-4,6-diones, a common feature pharmacophore model was constructed and validated. The rank score, fit value, enrichment factor (EF^20%), and receiver operating characteristic area under the curve (ROC-AUC) were used as validation metrics.

The NMPs were only active against S. aureus, with compound 3 (4 µg/ml) being the most active. The majority of NMPs were bacteriostatic. A common feature pharmacophore model was validated (rank score: 120.5; fit value: 4; EF^20%: 4.3; ROC-AUC: 0.9 ± 0.03) and showed that three hydrogen bond acceptors and a ring aromatic region are important for activity. Comparing the partition coefficient of the NMPs to their MIC a statistically significant correlation was found.

NMPs can be used as lead compounds in future studies. The validated pharmacophore model and partition coefficient can be used to develop more active compounds.

Infectious keratitis is a pernicious disease that affects the anterior segment of the eye and is one the leading causes of blindness worldwide. This disease may cause severe visual impairment or permanent vision damage if left untreated.

No doubt there are many conventional drug delivery systems to treat ocular keratitis, yet it is the fifth leading cause of blindness globally. This is the result of the eye's complex anatomy and barrier system, which restricts the total ocular contact time of the conventional formulations resulting in under-dosing. The widely used traditional formulations to treat keratitis, like antibiotic eye drops and ointments, are rendered useless due to less ocular contact time and low therapeutic drug levels at the target ocular site. The main requirement of the present time is to develop novel drug delivery-backed stratagems to overcome the shortcomings of conventional formulations, which will reduce the morbidity associated with infectious keratitis and improve clinical outcomes. It is worth mentioning that there are documented incidents of Herpetic keratitis of the cornea followed by COVID-19 infection and vaccination.

This paper is a rigorous review of all the novel drug delivery strategies to combat ocular keratitis. These future drug delivery strategies will pave the way for the present time researcher and formulation chemists to develop multi-dimensional novel formulations that are safe, patient-compliant, and surpass the ocular barriers to maintain therapeutic drug levels in ocular tissues.

Acquired Immunodeficiency Syndrome (AIDS) is one of most prevalent infectious diseases in the world, and HIV-1 protease (PR) is a vital target of drug design. Nowadays, three-dimensional quantitative structure-activity relationships (3D-QSAR) are applied to help design new protease inhibitions (PIs).

The primary objective of this study is to apply the 3D-QSAR study to a series of 42 derivatives of Darunavir (DRV) and to design new molecules possessing high antivirus activity.

Partial Least Squares (PLS) were used to cross-validate the dataset of compounds, and the optimal number of principal components (ONC), cross-validate coefficient (q²), standard error of estimate (SEE), non-cross-validated correlation coefficient (R²) and fisher test value (F) were calculated to assess model robustness. In this study, the CoMSIA-DAH model (q²=0.754, r²= 0.988, rpred²=0.57) possessed the highest predicted activity. Newly designed molecules were analyzed by docking studies with compound 25 taken as a template.

Within eight newly designed drugs, compound N02 possessed the highest antivirus activity (IC50=0.00461 nM) predicted by the CoMSIA-DAH model. The Surflex-Dock module of SYBYL-X 2.0 was used to affirm the predicted anti-PR activity of the newly designed compounds and the results of docking complex structure could be visualized. All newly designed molecules were in agreement with CSore above four and the docking study revealed that Asp29, Asp30, Ile50, Asp124, Asp128, Asp129 and Ile149 were critical residues in the process of inhibiting PR.

One of the main aspects of this study is the successful design of a series of molecules with excellent investigatory values, which elucidates explicit quantitative structure-activity relationships of DRV derivatives and will provide significant suggestions for future pharmaceutical research.

Modern pharmacological research indicated that Camellia nitidissima (CAM) had significant anti-tumor activity, but the investigation of its mechanism was still lacking.

The multi-component, multi-target and multi-pathway mechanism of CAM against tumor was investigated based on network pharmacology and molecular docking.

The active ingredients and targets of CAM were selected through a literature search, Traditional Chinese Medicine Systems Pharmacology database and PharmMapper database, and tumor-related targets were selected by GeneCards database, then to obtain the anti-tumor related targets of CAM. The protein interaction relationship was obtained through STRING database, protein-protein interaction network was constructed using Cytoscape 3.7.2 software, and enrichment analysis of GO and KEGG was conducted. AutoDock Tools 1.5.6 software was used to verify the molecular docking between the key ingredients and the key targets.

Catechin, epicatechin and luteolin were identified as the key anti-tumor related ingredients, and ESR1, EGFR, MAPK8, MAPK10, AR, PGR, F2 and PIK3CG were identified as the key targets. The GO entries mainly involved metabolic process, cellular process, response to stimulus, organelle, cytosol, etc. The KEGG enrichment showed that the key pathways included pathways in cancer, prostate cancer, pancreatic cancer, breast cancer, estrogen signaling pathway, MAPK signaling pathway, PI3K-Akt signaling pathway, etc. KEGG pathway maps indicated that the anti-tumor effect of CAM may be mainly achieved by intervening related targets in the following pathways: AR-HSP/AR-AR/PSA/proliferation and evading apoptosis; F2/GPCR/…/ROCK/tissue invasion and metastasis; F2/GPCR/…/Raf/MAPK signaling pathway/proliferation and sustained angiogenesis; EGFR/PI3K-Akt signaling pathway/proliferation, evading apoptosis and sustained angiogenesis; EGFR/Grb2/…/Raf/MAPK signaling pathway/proliferation and sustained angiogenesis; ER/Estrogen signaling pathway/proliferation; PR/PR-CoR/Wnts-RANKL/proliferation; oxidative stress (.O2-, .OH, H2O2)/KEAP1/NRF2/.../proliferation and evading apoptosis. The results of molecular docking showed that the key active ingredients had a good binding activity with each key target.

It was predicted that the main active ingredients of CAM could bind to tumor-related targets, such as receptor and coagulation-promoting factor, scavenge free radicals, and then interfere with the occurrence and development of tumors.

Pancreatic ductal adenocarcinoma (PDAC) is one of the leading causes of cancer-related deaths. Banzhilian (BZL) and Baihuasheshecao (BHSSC) are classical Chinese herbs used in tumor therapy. However, the underlying mechanisms of BZL-BHSSC in treating PDAC have not been identified. Combining network pharmacology with single-cell RNA sequencing (scRNA-seq), this study systematically explored the potential mechanisms of BZL-BHSSC in the treatment of PDAC.

The bioactive ingredients of BZL-BHSSC were screened from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) database, while the PDAC-related datasets were obtained from the Gene Expression Omnibus (GEO) database. Based on the dataset GSE62452, we adopted differential expression analysis and weighted gene co-expression network analysis (WGCNA) to screen the signature genes of PDAC. To reveal the cell types of the pharmacological targets of BZL-BHSSC against PDAC, we performed scRNA-seq analysis and principal component analysis (PCA) on the dataset GSE111672. Molecular docking and immunohistochemical staining were used to validate our initial results.

We obtained 29 bioactive ingredients from BZL-BHSSC and screened 210 signature genes of PDAC. Using network pharmacology, we identified 7 key therapeutic targets CDK1, MYC, CCNB1, TOP2A, CLDN4, NUF2, and MET, revealing that baicalein, quercetin, and luteolin are core components for the efficacy of BZL-BHSSC. The main signaling pathways involved in therapy were the PI3K-AKT signaling pathway and the p53 signaling pathway. The molecular docking results verified the strong binding activity (binding energy > -7 kJ/mol) between active ingredients and targets. The scRNA-seq results informed that cells from 3 PDAC samples could aggregate into 19 clusters and 3 cell types. The target genes were almost concentrated on the immune cells. Immuno-infiltration analysis suggested that the expression of Macrophages M0 and Dendritic cells activated was significantly upregulated in the PDAC group (p<0.001), while the opposite was true for B cells naïve and T cells CD8 expression (p<0.05).

We concluded that BZL-BHSSC can improve the overall survival prognosis of PDAC patients by interfering with the signature genes of PDAC through direct and indirect pathways and improving immunity. Our study provides a basis for subsequent studies.

The lead compounds isolated from medicinal plants constitute a matrix for research and discovery of new drugs using in silico study and molecular docking.

This work explores the in silico study and the molecular docking of two rare phytochemicals, namely Microphynolide A (1) and Microphynolide B (2), isolated from the Saharan medicinal plant Thymelaea microphylla (Thymelaeaceae family).

In the current work, several integrated web-based in silico pharmacokinetic tools were used to estimate the druggability of two isolated phytochemicals. In addition, molecular docking was conducted using AutoDockVina 4.2 to study the binding interactions with the targets predicted employing the PharmMapper server. The toxicological study was evaluated using ProTox-II online server. DFT methods were utilized to evaluate some physicochemical properties of structures, vibrational wavenumbers, and molecular electrostatic potentials.

Molecules (1) and (2) showed good ADMET profiles and antineoplastic activity. Also, they exhibited non-toxicity and belong to the Toxicity class VI (LD50 >8000 mg/kg) with immunotoxic activity. A good correlation was observed between the experimental and theoretical IR spectra, with no negative values in the theoretical spectra indicating the high stability of these compounds. Docking simulation studies against protein receptors Sulfotransferase 1A1 (PDB ID: 1LS6) and Angiogenin (PDB ID: 1B1I) displayed good binding affinity values of -5.8 and -6.8 kcal/mol, respectively, with number of H-bonding interactions. Furthermore, the control molecules p-Nitrophenol (pNP), Dopamine, Axitinib and Bevacizumab displayed values of binding energies of -6.7, -6.7, -6.9 and -6.3 Kcal/mol, respectively.

This study provides evidence supporting that the two molecules could be effective drugs to inhibit cancer cells and did not show any acute toxicity or mutagenic effects.

The prevalence of cancer in developing nations is a significant issue of concern. As a result of diverse global influences, this condition has surpassed coronary ailments to become the foremost cause of mortality. The role of PKM2 (Muscle Pyruvate Kinase 2) has garnered significant interest in the quest for agents in cancer progression. Flavonoids exhibit promise as a framework for the advancement of chemotherapeutic agents targeting cancer.

The principal aim of the present in silico investigation was to ascertain flavonoids as potential anticancer agents capable of inhibiting the PKM2 enzyme.

The preferred ligand molecules were docked to the human PKM2 enzyme using a computational molecular docking simulation technique to determine their affinity for the same enzyme. The molecular docking simulation was carried out using the AutoDock Vina software.

The chosen flavonoid docked well with the PKM2 enzyme, suggesting it may stimulate autophagy, hence acting as an anticancer agent.

In in silico studies, the chosen flavonoids showed a strong binding affinity, indicating that all of them impede the human PKM2 enzyme and have the potential to be used as cancer treatment alternatives.

β-Glucosidase has a variety of biological functions. A structural model for a potential β-glucosidase inhibitor has been proposed in the studies.

A series f new diaryl derivatives linked through benzimidazole have been randomly and rationally designed, synthesized, and evaluated for their inhibitory activities against β-glucosidase (almond). The proposed structural model provides a new strategy for the design of potent β-glucosidase inhibitors.

According to the model, a series of benzimidazole derivatives were designed and synthesized, and their inhibitory activity, Ki value, inhibitory type, and binding mode analysis (PDB ID: 2J7C) on β-glucosidase (almond) were evaluated.

Two compounds 7b and 7d were the best inhibitors with IC50 values of 7.86 μM and 3.52 μM, respectively. Their Ki values were calculated to be 9.91 μM and 5.81 μM, respectively.

The SAR analysis suggested that such benzimidazole derivatives might bind to the active site of β-glucosidase mainly through hydrogen bonds on o-trihydroxyphenol; the additional phenyl ring on the other side towards the solvent-exposed region played a very important role in improving their inhibitory activity against β-glucosidase.

The co-infection of HIV and abdominal TB poses a worldwide danger to humanity. This is because there are more strains of bacteria that are resistant to many classes of currently available medications. According to current findings, repurposing existing available medications will result in more effective functioning than using newly designed medications.

Based on this fact, we hypothesised that the PI could be repurposed; we used Food and Drug Administration (FDA)-approved PI drugs to treat HIV co-infected patients with abdominal TB, and a computational study has been conducted.

This comprises network analysis models to find their protein drug interaction (PDI) through a search tool for interacting chemicals (STICH) module of Cytoscape network analysis model followed by the screening of these drugs for their ADMET prediction and binding affinity with adenosine deaminase (ADA), a protein responsible for abdominal TB, and the HIV-1 Nef protein, responsible for the regulation of immune function (CD4⁺).

The network analysis showed 13 nearest binding drugs of these proteins of interest. The ADMET study result showed the pharmacologically relevant parameters that have a significant effect on the binding affinity, bioavailability, and toxicity of PI. The top three scores achieved by PI against adenosine deaminase enzyme activity (PDB ID: 1A4M) are viz., -23.7919, -23.3529, and -22.6773 for Ritonavir, Tipranavir, and Atazanavir, respectively. The top three scores achieved by PI against HIV-1 Nef protein activity (PDB ID: 6URI) are viz., -28.7321, -28.4987, and -28.3155 for Atazanavir, Tipranavir, and Simeprevir, respectively. The active site of ADA and HIV-1 Nef proteins comprises amino acid residues such as for Tipranavir: Arene-Cation interaction (Phenyl and Pyridine)- Arg B1081, and Lys B1033 (1A4M) and Arene-Cation interaction (Pyridine and Phenyl)- Lys D11 and Arg D33; Sidechain acceptor Thr B40; Sidechain donor- Asp D30; Backbone donor- Ala B37 (6URI). Atazanavir: Arene-Cation interaction (Phenyl)- Lys A254 and Lys B1033; Sidechain acceptor - Arg A251 (1A4M).

Thus, from the computational studies carried out, we could obtain hints for optimising the molecular selectivity of the PI to provide help in the design of new compounds via the repurposing strategy of the FDA-approved PI for effective treatment of co-morbidity with HIV and abdominal TB. However, further pharmacokinetics, pharmacodynamics, preclinical, and clinical studies permit the design of the new agents without undesirable interactions.

The activated oncogenic Notch signalling is an emerging target to treat cancer progression and recurrence. Synthetic inhibitors of Notch receptors are in pre-clinical studies. However, the overexpression of Notch signalling molecules at the gene level needs to be regulated to control cancer progression.

We propose that this can be achieved by gene-regulatory drugs in combination with natural phytochemical compounds.

The ethanol extract of Allium sativum alone and in combination with DAPT and ATRA were evaluated for cytotoxicity on A549 cells by MTT and Trypan blue assays. Their effects on Notch 1, Hes 1 and p53 gene expressions were studied by RT-PCR and qPCR. Their inhibition on metastatic invasion of A549 cells was analyzed by in vitro wound scratch assay. The phytochemicals of the extract were identified by GC-MS analysis.

Many organosulfur compounds having anti-cancer potency were identified in GC-MS. The combination treatment with 50µg (IC50) of garlic extract exhibited a highly significant (P≤0.01) synergistic inhibitory effect on A549 cell growth and migration. It has also significantly reduced the expression of Notch 1 and Hes 1 oncogenes and enhanced p53 gene expression, compared with the individual treatments. This indicates the synergistic action of the extract on the downregulation of Notch signalling at the mRNA level.

Our study results imply that the combination therapies have potent molecular treatment action via down-regulating Notch signaling target genes and upregulating p53 gene expression as an underlying mechanism of inhibitory action on A549 lung cancer cells.

Nowadays, inflammation is recognized as the underlying cause of a number of diseases, but NSAIDs are the first drug of choice, having several side effects. Additionally, excessive cellular oxidative stress is often considered a major contributor to pathophysiological conditions, the development of cancer, and other diseases. Antimicrobial resistance is a global concern, hence, there is a critical need for the development of novel therapeutic agents to fight the emergence and increasing prevalence of resistant pathogens. This creates an initiation to introduce new molecules which act as efficient therapeutic agents with diminished side effects.

As a part of our search for newer agents with enhanced activity profiles, it was planned to synthesize novel 2- (benzamido)-N-((benzo[d][1,3]dioxol-4-yl)methylene)-3-(substituted phenyl) acrylohydrazides and to investigate them for antiinflammatory, antioxidant, cytotoxic, antimicrobial activities. Furthermore, in silico studies were performed for title compounds to predict molecular properties, bioavailability, drug-likeness, and bioactivity scores, molecular docking studies were also performed against biological targets.

The title compounds 1-14 were synthesized by nucleophilic addition of piperonal in ethanol, few drops of acetic acid to the intermediate 2-(benzamido)-3-(aryl)acrylohydrazides. The title compounds were tested for their antiinflammatory activity by in vivo carrageenan-induced rat paw edema method, in vitro COX-2 inhibition assay; in vitro cytotoxic activity evaluation by MTT assay; antioxidant activity by Lipid peroxidation, DPPH assay, Nitric Oxide scavenging assay and Hydrogen peroxide scavenging assay; and antimicrobial activity by cup plate method. Physicochemical properties and bioactive scores of title compounds were evaluated by in silico studies. Molecular docking studies were carried out for the title compounds against COX-2 (PDB: 5F19) and EGFR (PDB:1XKK).

Among the series, 4-Hydroxy-3,5-dimethoxy derivative (5) displayed good anti-inflammatory and antioxidant activities; Vanillinyl derivative (4) displayed good cytotoxicity and antimicrobial activity when compared to that of the respective standards. Compounds 5 & 4 also exhibited good docking scores with COX-2 and EGFR, respectively. All title compounds obeyed Lipinski’s rule of five and also exhibited acceptable molecular properties, drug-likeness properties, and moderate to good bioactivity scores in in silico studies.

The study suggested that the title compounds showed notable pharmacological properties, could emerge as lead compounds, and be further explored as promising therapeutic agents.

Fruits like berries are known not only for their taste and nutritional value but also for the potential health benefits of their bioactive components. Stilbenes, a group of phenolic metabolites found in berries, demonstrate significant pharmacological activities. Its derivatives also have been investigated for their biological functions, including as anticancer agents. Bcl-2 antiapoptotic proteins are highly involved in regulating cancer progression by promoting apoptosis evasion. Hence, Bcl-2 is a promising therapeutic target in drug development.

This study aimed to determine the stilbene derivatives with the best potential as Bcl-2 inhibitors.

The method used was molecular docking of several stilbene derivatives to Bcl-2 receptors using AutoDock 4.2, followed by an ADMET study.

Based on the docking score and ligand-receptor interactions, oxyresveratol and pterostilbene had the best docking findings for the Bcl-2 antiapoptotic proteins. Among these eleven substances, pterostilbene significantly inhibited Bcl-w and Mcl-1, whereas oxresveratrol could inhibit Bcl-2. Although the findings from the two ADMET profiles were varied, further in vitro and in vivo studies are required to explore the potential of the compounds.

In conclusion, the study identified the potential chemopreventive agents, such as pterostilbene and oxyresveratrol might serve as potential lead compounds for developing new Bcl-2 inhibitors.

Non-alcoholic fatty liver disease (NAFLD) is considered the most common liver disease. Shugan Jiangzhi Decoction (SJD), a traditional Chinese medicine (TCM) formula which consists of six Chinese herbs, has been used for treating hyperlipidemia, obesity, and fatty liver in Guangdong Provincial Hospital of Traditional Chinese Medicine for over twenty years.

This study aims to elucidate the chemical basis and the molecular mechanism of SJD against NAFLD.

The main components of SJD were determined by High Performance Liquid Chromatography (HPLC). Then the high-fat diet (HFD)-induced NAFLD rat model was established. After treatment with different doses of SJD, the body weight of rats was measured weekly. On the last day of the experiments, the hepatic morphology, histopathology changes, and the serum lipid levels were detected. Then techniques of network pharmacology were employed to predict the anti-NAFLD mechanism of SJD. At last, the expression levels of proteins were measured by western blot to verify the mechanism.

Nine chemical constituents of SJD were identified from HPLC fingerprint spectrum. For the in vivo experiment, NAFLD rat model was constructed successfully by feeding high-fat diet (HFD) for 8 weeks. The following treatment with SJD for 6 weeks decreased the fatty droplet accumulation in the liver obviously. Meanwhile, the serum level of high-density lipoprotein cholesterol (HDL-c) was increased, while the levels of low-density lipoprotein cholesterol (LDL-c), aspartate aminotransferase (AST), and alanine aminotransferase (ALT) were decreased after SJD treatment (p < 0.05). The results of network pharmacology indicated that SJD might improve NAFLD via regulating the AMPK/PPAR signaling pathway. Then, the western blot assay confirmed that SJD activated the AMPK/PPAR signaling pathway in the liver of rats.

SJD improves HFD-induced NAFLD in rats via AMPK/PPAR signaling pathway. Thus, our study suggests that SJD can serve as a therapeutic agent for the prevention and treatment of NAFLD.

The clinical applications of platinum-based anticancer drugs are largely compromised by side effects and drug resistance. Therefore, novel platinum-based anticancer drugs with improved injected or oral therapeutic index and low resistance need to be developed.

This study aimed at the synthesis and anticancer activity testing of Pt(IV) prodrugs containing α-furancarboxylate as an axial ligand. This would pave the way for obtaining novel Pt(IV) prodrugs with better anticancer activity by comparing the anticancer activity with their parent platinum(II) complexes.

In this study, synthesis, in vitro cytoxicity assay, and in vivo anticancer activity evaluation of three Pt(IV) complexes, cis,trans,cis-[Pt(NH3)2(OH)(α-furancarboxylato)Cl2] (FPt-1), cis,trans,cis-[Pt(NH3)2(OH)(α-furancarboxylato)(1,1'-cylobutanedicarboxylato)] (FPt-2), and cis,trans,cis-[Pt(1R,2R-diaminocyclohexane)(OH)(α-furancarboxylato)(C2O4)] (FPt-3), were carried out.

Three Pt(IV) complexes exhibited considerable cytoxicity against the tested human cancer cells (MCF-7, A549 and HCT116), which was found to be slightly lower than the corresponding Pt(II) drugs. However, FPt-1 and FPt-3 displayed comparable antitumor efficacy to cisplatin and oxaliplatin in the murine S180 sarcoma model after intraperitoneal administration. More importantly, the intragastric administration test indicated the antitumor efficacy of FPt-3 to be much greater than oxaliplatin.

FPt-3 has shown excellent oral antitumor activity and it could be administrated in an oral dosage form.