In silico Exploration of a Novel ICMT Inhibitor with More Solubility than Cysmethynil against Membrane Localization of KRAS Mutant in Colorectal Cancer.

BACKGROUND: ICMT (isoprenylcysteine carboxyl methyltransferase) is an enzyme that plays a key role in the post-translational modification of the K-Ras protein. The carboxyl methylation of this protein by ICMT is important for its proper localization and function. Cysmethynil (2-[5-(3-methylphenyl)-l-octyl-lH-indolo-3-yl] acetamide) causes K-Ras mislocalization and interrupts pathways that control cancer cell growth and division through inhibition of ICMT, but its poor water solubility makes it difficult and impractical for clinical use. This indicates that relatively high amounts of cysmethynil would be required to achieve an effective dose, which could result in significant adverse effects in patients. OBJECTIVE: The general objective of this work was to find virtually new compounds that present high solubility in water and are similar to the pharmacological activity of cysmethynil. METHODS: Pharmacophore modeling, pharmacophore-based virtual screening, prediction of ADMET properties (absorption, distribution, metabolism, excretion, and toxicity), and water solubility were performed to recover a water-soluble molecule that shares the same chemical characteristics as cysmethynil using Discovery Studio v16.1.0 (DS16.1), SwissADME server, and pkCSM. RESULTS: In this study, ten pharmacophore model hypotheses were generated by exploiting the characteristics of cysmethynil. The pharmacophore model validated by the set test method was used to screen the "Elite Library®" and "Synergy Library" databases of Asinex. Only 1533 compounds corresponding to all the characteristics of the pharmacophore were retained. Then, the aqueous solubility in water at 25°C of these 1533 compounds was predicted by the Cheng and Merz model. Among these 1533 compounds, two had the optimal water solubility. Finally, the ADMET properties and Log S water solubility by three models (ESOL, Ali, and SILICOS-IT) of the two compounds and cysmethynil were compared, resulting in compound 2 as a potential inhibitor of ICMT. CONCLUSION: According to the results obtained, the identified compound presented a high solubility in water and could be similar to the pharmacological activity of cysmethynil.

Exploration of Novel PDEδ Inhibitor Based on Pharmacophore and Molecular Docking against KRAS Mutant in Colorectal Cancer.

AIM: The prenyl-binding protein, phosphodiesterase-δ (PDEδ), is essential for the localization of prenylated KRas to the plasma membrane for its signaling in cancer. INTRODUCTION: The general objective of this work was to develop virtually new potential inhibitors of the PDEδ protein that prevent Ras enrichment at the plasma membrane. METHODS: All computational molecular modeling studies were performed by Molecular Operating Environment (MOE). In this study, sixteen crystal structures of PDEδ in complex with fifteen different fragment inhibitors were used in the protein-ligand interaction fingerprints (PLIF) study to identify the chemical features responsible for the inhibition of the PDEδ protein. Based on these chemical characteristics, a pharmacophore with representative characteristics was obtained for screening the BindingDB database. Compounds that matched the pharmacophore model were filtered by the Lipinski filter. The ADMET properties of the compounds that passed the Lipinski filter were predicted by the Swiss ADME webserver and by the ProTox-II-Prediction of Toxicity of Chemicals web server. The selected compounds were subjected to a molecular docking study. RESULTS: In the PLIF study, it was shown that the fifteen inhibitors formed interactions with residues Met20, Trp32, Ile53, Cys56, Lys57, Arg61, Gln78, Val80, Glu88, Ile109, Ala11, Met117, Met118, Ile129, Thr131, and Tyr149 of the prenyl-binding pocket of PDEδ. Based on these chemical features, a pharmacophore with representative characteristics was composed of three bond acceptors, two hydrophobic elements, and one hydrogen bond donor. When the pharmacophore model was used in the virtual screening of the Binding DB database, 2532 compounds were selected. Then, the 2532 compounds were screened by the Lipinski rule filter. Among the 2532 compounds, two compounds met the Lipinski's rule. Subsequently, a comparison of the ADMET properties and the drug properties of the two compounds was performed. Finally, compound 2 was selected for molecular docking analysis and as a potential inhibitor against PDEδ. CONCLUSION: The hit found by the combination of structure-based pharmacophore generation, pharmacophore- based virtual screening, and molecular docking showed interaction with key amino acids in the hydrophobic pocket of PDEδ, leading to the discovery of a novel scaffold as a potential inhibitor of PDEδ.

Withdrawal Notice: Identification of the Interaction between Angiotensin-converting Enzyme Residues and Severe Acute Respiratory Syndrome Coronavirus 2

The article has been withdrawn by the Editorial office of the journal Current Pharmaceutical Design. The decision is reached by all authors, for below reasons: • Data been published should be updated. • New approach of this study and new results mentioning the vaccine and its interaction with ACE2. Bentham Science apologizes to the readers of the journal for any inconvenience this may have caused. The Bentham Editorial Policy on Article Withdrawal can be found at https://benthamscience.com/editorial-policies-main.php. BENTHAM SCIENCE DISCLAIMER: It is a condition of publication that manuscripts submitted to this journal have not been published and will not be simultaneously submitted or published elsewhere. Furthermore, any data, illustration, structure or table that has been published elsewhere must be reported, and copyright permission for reproduction must be obtained. Plagiarism is strictly forbidden, and by submitting the article for publication the authors agree that the publishers have the legal right to take appropriate action against the authors, if plagiarism or fabricated information is discovered. By submitting a manuscript, the authors agree that the copyright of their article is transferred to the publishers if and when the article is accepted for publication.

In Silico Investigation of the SARS CoV2 Protease with Thymoquinone, the Major Constituent of Nigella Sativa.

INTRODUCTION: The COVID-19 caused by a new type of coronavirus has emerged from China and led to thousands of deaths globally. Despite many groups engaged in studying the newly emerged virus and searching for the treatment, the understanding of the SARS-CoV2 target ligand interactions represents a key challenge. Several studies are being conducted to identify potential treatment. Alternatively, the results of numerous studies have shown that protease inhibitors can be a genuine leader in research. The antiviral activity and beneficial effect against respiratory disorders of thymoquinone have been largely demonstrated. AIM: The aim of this study is to evaluate in silico the inhibition of the replication of SARS CoV2 by thymoquinone. METHODS: This is a molecular simulation study using SARS CoV2 protease and thymoquinone structures provided by Protein Data Bank. RESULTS: The preliminary results have shown that thymoquinone may have inhibitory activities against SARS CoV2 protease. CONCLUSION: Furthermore, given the demonstrated results of thymoquinone, we can conclude that it may be considered as an effective or adjuvant treatment for SARS CoV2 infection.