Molecular modeling provides a structural basis for PERK inhibitor selectivity towards RIPK1

RIPK1 inhibitors: A key to unlocking the potential of necroptosis in drug development

Within the field of medical science, there is a great deal of interest in investigating cell death pathways in the hopes of discovering new drugs. Over the past two decades, pharmacological research has focused on necroptosis, a cell death process that has just been discovered. Receptor-interacting protein kinase 1 (RIPK1), an essential regulator in the cell death receptor signalling pathway, has been shown to be involved in the regulation of important events, including necrosis, inflammation, and apoptosis. Therefore, researching necroptosis inhibitors offers novel ways to treat a variety of disorders that are not well-treated by the therapeutic medications now on the market. The research and medicinal potential of RIPK1 inhibitors, a promising class of drugs, are thoroughly examined in this study. The journey from the discovery of Necrostatin-1 (Nec-1) to the recent advancements in RIPK1 inhibitors is marked by significant progress, highlighting the integration of traditional medicinal chemistry approaches with modern technologies like high-throughput screening and DNA-encoded library technology. This review presents a thorough exploration of the development and therapeutic potential of RIPK1 inhibitors, a promising class of compounds. Simultaneously, this review highlights the complex roles of RIPK1 in various pathological conditions and discusses potential inhibitors discovered through diverse pathways, emphasizing their efficacy against multiple disease models, providing significant guidance for the expansion of knowledge about RIPK1 and its inhibitors to develop more selective, potent, and safe therapeutic agents.

Evidence for paraquat-pepsin interaction: In vitro and silico study

The use of the herbicide paraquat (PQ) has raised concerns about potential environmental consequences due to its toxicity and persistence in the environment. Considering the affinity of dangerous compounds to biological molecules, it is necessary to know their binding properties. This article focuses on the behavior of the pepsin enzyme following its contact with paraquat poison, and the interaction between paraquat and pepsin has been investigated in laboratory conditions and simulated physiological conditions using multispectral techniques. Fluorescence experiments showed that PQ uses a static method to quench pepsin's intrinsic fluorescence. By causing structural damage to pepsin, PQ may be detrimental as it alters its conformational function based on FT-IR spectroscopy. The coupling reaction is a spontaneous process caused by hydrogen bonding and van der Waals forces according to the analysis of the thermodynamic parameters of each system at three different temperatures. The molecular structure of pepsin changes when it binds to PQ. Also, the results showed that PQ is a pepsin inhibitor that changes the function of the enzyme.

GSK2606414 Sensitizes ABCG2-Overexpressing Multidrug-Resistant Colorectal Cancer Cells to Chemotherapeutic Drugs

Colorectal cancer is a common malignant tumor. A major factor in the high mortality rate of colorectal cancer is the emergence of multidrug resistance (MDR). Overexpression of the ABCG2 gene in cancer cells directly leads to MDR. Finding new inhibitors of ABCG2 may be an effective way to overcome drug resistance. We found that the compound GSK2606414 enhanced the sensitivity of the ABCG2 substrate to the chemotherapeutic drugs mitoxantrone and doxorubicin in ABCG2-overexpressing multidrug-resistant colorectal cancer cells by increasing their intracellular accumulation without affecting the protein expression of ABCG2. Molecular docking experiments predicted that GSK2606414 could stably bind in the drug-binding pocket of ABCG2. In conclusion, GSK2606414 can sensitize ABCG2-overexpressed multidrug-resistant colorectal cancer cells to chemotherapy drugs and can be used as a potential inhibitor of ABCG2.

Different protective capability of chlorogenic acid and quercetin against indomethacin-induced gastrointestinal ulceration

OBJECTIVES

The study compared the protective effects against indomethacin-induced GI ulceration of chlorogenic acid with quercetin in rats.

METHODS

Rats were orally given chlorogenic acid or quercetin (100 mg/kg; 5 days), followed by indomethacin (40 mg/kg; single dose). After 24 h, GI tissues were assessed for histopathological damages, then analysed by ELISA and western blot methods. Cell viability was measured in vitro by MTT assay.

KEY FINDINGS

Unlike quercetin, chlorogenic acid could not prevent gastric ulcers in indomethacin-treated rats. The levels of gastric prostaglandin E2 (PGE2) and Bax/Bcl-2 ratio in the chlorogenic acid-treated group were not different from those receiving indomethacin alone. Nevertheless, both compounds alleviated jejunum ulcers through suppression of PERK/eIF-2/ATF-4/CHOP-related endoplasmic reticulum (ER) stress and decrease Bax/Bcl-2 ratio. Moreover, at 100 µM, they abolished the cytotoxicity of tunicamycin (an ER stress inducer) in gastric (AGS) and intestinal (Caco-2) cells. In silico docking studies suggested that both compounds could interact with key amino acid residues in the -catalytic domain of PERK.

CONCLUSION

Chlorogenic acid and quercetin exerted comparable protective effects against indomethacin-induced intestinal ulcer through suppression of ER stress-mediated apoptosis but, unlike quercetin, chlorogenic acid offered no protection against gastric ulceration due to its -inability to increase PGE2 production.

Computational Study of Bis-(1-(Benzoyl)-3-Methyl Thiourea) Platinum (II) Complex Derivatives as Anticancer Candidates

Background

The increasing incidence of cancer every year has resulted in cancer becoming one of the most common causes of death in the world. The most common types of cancer are breast cancer, lung cancer and prostate cancer. Thiourea is one of the compounds that have anticancer effects, and its activity can be increased by structural modifications, one of which involves making a Bis-(1-(benzoyl)-3-methyl thiourea) platinum (II) metal complex.

Purpose

This study aims to obtain platinum (II)-thiourea complex compounds that have a more stable interaction as an anticancer agent compared to cisplatin.

Methods

The methods used are computational studies with molecular docking, simulation of molecular dynamics, and prediction of pharmacokinetics and toxicity.

Results

Based on the molecular docking of the platinum (II)-thiourea complex which has the most stable interaction with lower binding energy than the native ligand and the cisplatin, namely Bis-(3-methyl-1-(naphthalene-2-carbonyl)thiourea)) Platinum (II) against breast cancer receptors (3ERT) and lung cancer (2ITO) and compounds Bis-(1-(3-chlorobenzoyl)-3-methylthiourea) Platinum (II) against prostate cancer receptors (1Z95). The evaluation results of the stability of the interaction using a 50 ns molecular dynamic simulation showed that the Bis-(1-benzoyl-3-methylthiourea) Platinum (II) which binds to the prostate cancer receptor (1Z95) has the most stable interaction. Pharmacokinetic prediction results show that the platinum (II)-thiourea complex has a good pharmacokinetic profile, but there are several compounds that are mutagenic and hepatotoxic.

Conclusion

The Bis-(1-(3,4-dichlorobenzoyl)-3-methyl thiourea) platinum (II) compounds could be a suitable anticancer agent for the lungs.

Identification of common genes in obesity and cancer through network interaction and targeting those genes by virtual screening approach

Obesity may have an effect on cancer outcomes, resulting in global inequalities in cancer survival and death. Microarray data analysis was done to identify differentially expressed genes (DEGs) in obese and cancer patients. Total 1977 differentially expressed genes among obesity and gastric cancer, breast cancer, pancreatic cancer, and colorectal cancer were used to build a gene interaction network, which was then analyzed by using Cytoscape software. It has been identified that JUN, CXCL12, and LEP genes show a higher degree and stress, and play an important role in obesity and cancer progression. Further, CXCL12 and LEP were taken for virtual screening study with coumarin and its derivatives to develop a drug against obesity and cancer. The interactions of CXCL12 and LEP with coumarins were studied by molecular docking and it shows good interaction as well as docking score as compared to the standard one. The ADME properties were predicted to check the drug-likeness activity of coumarins and the most of the drug-likeness activities are in admire range. The Binding free energy of the docked complex was calculated by performing MM-GBSA. The molecular docking, ADME properties prediction, and MM-GBSA was performed on Maestro 12.6. The top docked score compounds were further subjected to molecular dynamic simulation to check the stability by using GROMACS. The MM-PBSA study was performed to calculate the binding energy components as well as the energy contributions of specific amino acids. The resultant compounds could be a potent anti-obesity and anti-cancer drug.Communicated by Ramaswamy H. Sarma.

From PERK to RIPK1: Design, synthesis and evaluation of novel potent and selective necroptosis inhibitors

Receptor-Interacting serine/threonine-Protein Kinase 1 (RIPK1) emerged as an important driver of inflammation and, consequently, inflammatory pathologies. The enzymatic activity of RIPK1 is known to indirectly promote inflammation by triggering cell death, in the form of apoptosis, necroptosis and pyroptosis. Small molecule Receptor-Interacting serine/threonine-Protein Kinase 1 inhibitors have therefore recently entered clinical trials for the treatment of a subset of inflammatory pathologies. We previously identified GSK2656157 (GSK'157), a supposedly specific inhibitor of protein kinase R (PKR)-like ER kinase (PERK), as a much more potent type II Receptor-Interacting serine/threonine-Protein Kinase 1 inhibitor. We now performed further structural optimisation on the GSK'157 scaffold in order to develop a novel class of more selective Receptor-Interacting serine/threonine-Protein Kinase 1 inhibitors. Based on a structure-activity relationship (SAR) reported in the literature, we anticipated that introducing a substituent on the para-position of the pyridinyl ring would decrease the interaction with PERK. Herein, we report a series of novel GSK'157 analogues with different para-substituents with increased selectivity for Receptor-Interacting serine/threonine-Protein Kinase 1. The optimisation led to UAMC-3861 as the best compound of this series in terms of activity and selectivity for Receptor-Interacting serine/threonine-Protein Kinase 1 over PERK. The most selective compounds were screened in vitro for their ability to inhibit RIPK1-dependent apoptosis and necroptosis. With this work, we successfully synthesised a novel series of potent and selective type II Receptor-Interacting serine/threonine-Protein Kinase 1 inhibitors based on the GSK'157 scaffold.

In silico analytical toolset for predictive degradation and toxicity of hazardous pollutants in water sources

Different phenolic compounds, including multimeric lignin derivatives in the β-O-4 form, are among the most prevalent compounds in wastewater, often generated from paper industries. Relatively small concentrations of lignin are hazardous to aquatic organisms and can trigger severe environmental hazards. Herein, we present a predictive toolset to insight the induced toxic hazards prediction, and their Lignin peroxidase (LiP)-assisted degradation mechanism of selected multimeric lignin model compounds. T.E.ST and Toxtree toolset were deployed for toxic hazards estimation in different endpoints. To minimize the concerning hazards, we screened multimeric compounds for binding affinity with LiP. The binding affinity was found to be significantly lower than the reference compound. An Extra precision (XP) Glide score of -6.796 kcal/mol was found for dimer (guaiacyl 4-O-5 guaiacyl) complex as lowest compared to reference compound (-4.007 kcal/mol). The active site residues ASP-153, HIP-226, VAL-227, ARG-244, GLU-215, 239, PHE-261 were identified as site-specific key binding AA residues actively involved with corresponding ligands, forming Hydrophobic, H-Bond, π-Stacking, π-π type interactions. The DESMOND-assisted molecular dynamics simulation's (MDS) trajectories of protein-ligand revealed the considerable binding behavior and attained stability and system equilibrium state. Such theoretical and predictive conclusions indicted the feasibility of LiP assisted sustainable mitigation of lignin-based compounds, and such could be used to protect the environment from the potential hazards posed by recognized similar pollutants.

Computational Studies of Thiourea Derivatives as Anticancer Candidates through Inhibition of Sirtuin-1 (SIRT1)

Cancer is a disease that starts from the uncontrolled growth of abnormal cells in the organs or tissues of the body, which is the second leading cause of death in the world. One of the targets in discovering and developing anticancer drugs is Sirtuin-1. SIRT1 can act as a tumor suppressor or tumor promoter depending on its target in a particular signalling pathway or on particular cancer. This study aimed to study the interaction of a thiourea derivative with SIRT1 (PDB ID:4I5I) through its inhibition of histone deacetylase. Research has been carried out in silico with molecular docking (MGLTools.1.5.6) and molecular dynamics (Desmond 2019) of three thiourea derivatives to the receptor. In addition, pharmacokinetic parameters, toxicity, and selection of Lipinski's Rule of Five were also tested. Molecular docking results showed that compound b ([2-(methylcarbamothioylcarbamoyl)phenyl]benzoate) had the lowest ∆G value of −9.29 kcal/mol with a KI value of 0.156 µM compared to other thiourea derivatives and was proven by molecular dynamics tests for 30 ns and amino acids that play an active role in the interaction include the residue PheA:297. In terms of pharmacokinetics and toxicity, compound b is better than natural ligands. Compound b is predicted to be used as an anticancer candidate through further research.