In silico Drug Repurposing of Anticancer Drug 5-FU and Analogues Against SARS-CoV-2 Main Protease: Molecular Docking, Molecular Dynamics Simulation, Pharmacokinetics and Chemical Reactivity Studies

Design, Synthesis, and Biological Studies of C-5-Substituted Diazenyl Derivatives of Uracil as Potent and Selective Antileishmanial Agents Targeting Uridine Biosynthesis Pathway Enzymes

Herein, we describe the design and synthesis of a series of C-5-substituted diazenyl derivatives of uracil, exhibiting selective and potent antileishmanial but not antibacterial or antifungal activity. The formation of the substituted derivatives was confirmed by using FTIR, 1H, 13C NMR, and HRMS analysis. Among all of the sets of tested compounds, only three [4a, 6b, and 8b] showed the highest activity against Leishmania donovani (LD) promastigote and amastigote models of LD infections. Further, the cytotoxicity assays performed using three different cell lines, Vero cells, J774 cells, and THP1 cells, along with erythrocyte hemolysis assay showed the highest biocompatibility for the 4a, making it a lead compound for further biological assays. The LD cell death associated with 4a was not linked with ergosterol depletion, a common mechanism of action of antileishmanial drugs like amphotericin B (AmB). However, the LD cell death in the presence of 4a was reversed significantly through supplementation of uridine monophosphate (UMP), indicating the specific role of uridine biosynthesis pathway as the target of 4a. Furthermore, the in silico studies predicted orotidine monophosphate decarboxylase enzyme (OMPDCase) from LD as the plausible target for 4a. The proteomics analysis showed stronger downregulation of the aforementioned OMPDCase and also for a few other enzymes that are involved in the UMP biosynthesis pathway. This indicates that OMPDCase and other enzymes that regulate the UMP biosynthesis may be the target of 4a. Overall, the C-5-substituted diazenyl derivatives of uracil are presented here as novel and potent antileishmanial agents that can be used for treating visceral leishmaniasis (VL) wherein at present drug resistance and side effects of existing drugs demand a look for safer alternatives.

Explore on screening COX-2 inhibitors from the essential oil of Solanum lyratum Thunb. By molecular docking and molecular dynamics simulation

This study aimed to investigate Solanum lyratum Thunb. with respect to the potential ingredients with anti-inflammatory activity from its essential oil by silico study. To this regard, the essential oil of Solanum lyratum Thunb. was extracted by hydrodistillation. 25 compounds were identified by GC-MS. Using virtual screening, molecular docking and molecular dynamics simulation of the 25 identified compounds, the ones showing anti-inflammatory activity on COX-2 were identified. According to the drug-like principle and the prediction of ADEMT properties, the six compounds of Spathulenol, Cedrol, Juniper camphor, Santalol, Nootkatone and 7,9-Di-tert-butyl-1-oxaspiro[4.5]deca-6,9-diene-2,8-dione were identified and then studied for molecular docking, and based on which the top two compounds of binding free energy were studied by the molecular dynamics simulation. The molecular docking data indicated that the binding free energies of Spathulenol, Cedrol, Juniper camphor, Santalol, Nootkatone and 7,9-Di-tert-butyl-1-oxaspiro[4.5]deca-6,9-diene-2,8-dione to COX-2 protein were -5.65, -7.19, -6.35, -4.94, -5.82 and -5.14 kcal/mol, respectively. The findings showed the steady interactions of hydrogen bonds and hydrophobic bonds between both the top two compounds of binding free energy and the active site residues of COX-2 (4M11) throughout the simulation via hydrogen bonds and hydrophobic bonds. The very study shall be supportive for in vitro and in vivo studies in developing drug products using the lead bioactive ingredients for anti-inflammatory in the future.

Bioinformatics Study of Flavonoids From Genus Erythrina As Ace2 inhibitor Candidates For Covid-19 Treatment

Purpose

This study aimed to screen potential drug candidates from the flavonoids of the genus Erythrina for the Corona Virus Disease 2019 (COVID-19) treatment.

Patients and Methods

A comprehensive screening was conducted on the structures of 473 flavonoids derived from the genus Erythrina, focusing on their potential toxicity and pharmacokinetic profiles. Subsequently, flavonoids that were non-toxic and possessed favorable pharmacokinetic properties underwent further analysis to explore their interactions with the angiotensin-converting enzyme 2 (ACE2) receptor, employing molecular docking and molecular dynamics simulations.

Results

Among 473 flavonoids, 104 were predicted to be safe from being mutagenic, hepatotoxic, and inhibitors of the human ether-a-go-go-related gene (hERG). Among these 104 flavonoids, 18 compounds were predicted not to be substrates of P-glycoprotein (P-gp). Among these 18 flavonoids, gangetinin (471) and erybraedin D (310) exhibit low binding affinities and root mean square deviation (RMSD) values, indicating stable binding to the ACE2 receptor. The physicochemical attributes of compounds 310 and 471 suggest that they possess drug-like properties.

Conclusion

Gangetinin (471) and erybraedin D (310) may serve as promising candidates for COVID-19 treatment due to their potential to inhibit the ACE2-RBD interaction. This warrants further investigation into their inhibitory effects on ACE2-RBD binding through in vitro experiments.

Predictive Modelling in pharmacokinetics: from in-silico simulations to personalized medicine

INTRODUCTION

Pharmacokinetic parameters assessment is a critical aspect of drug discovery and development, yet challenges persist due to limited training data. Despite advancements in machine learning and in-silico predictions, scarcity of data hampers accurate prediction of drug candidates' pharmacokinetic properties.

AREAS COVERED

The study highlights current developments in human pharmacokinetic prediction, talks about attempts to apply synthetic approaches for molecular design, and searches several databases, including Scopus, PubMed, Web of Science, and Google Scholar. The article stresses importance of rigorous analysis of machine learning model performance in assessing progress and explores molecular modeling (MM) techniques, descriptors, and mathematical approaches. Transitioning to clinical drug development, article highlights AI (Artificial Intelligence) based computer models optimizing trial design, patient selection, dosing strategies, and biomarker identification. In-silico models, including molecular interactomes and virtual patients, predict drug performance across diverse profiles, underlining the need to align model results with clinical studies for reliability. Specialized training for human specialists in navigating predictive models is deemed critical. Pharmacogenomics, integral to personalized medicine, utilizes predictive modeling to anticipate patient responses, contributing to more efficient healthcare system. Challenges in realizing potential of predictive modeling, including ethical considerations and data privacy concerns, are acknowledged.

EXPERT OPINION

AI models are crucial in drug development, optimizing trials, patient selection, dosing, and biomarker identification and hold promise for streamlining clinical investigations.

SARS-CoV-2 Mpro binding profile and drug-likeness of two novel thiazole derivatives: structural elucidation, DFT studies, ADME-T and molecular docking simulations

Two novel thiazole derivatives, ethyl 5-((4-fluorophenyl)carbamoyl)-thiazole-4-carboxylate (2b) and ethyl 5-(p-tolylcarbamoyl)thiazole-4-carboxylate (6b) have been synthesized, and their crystal structures determined by X-ray diffraction. To rationalize their structure, reactivity and druggability, we have performed a series of separate, but complementary studies. Hirshfeld surface and 2D-fingerprint plots were first scrutinized to qualitatively unveil all the intermolecular interactions that ensure their crystal packing. Moreover, topological electron density parameters established from the quantum theory of atoms-in-molecules (QTAIM) and Reduced Density Gradient (RDG) were later relied on to characterize the chemical bonding of these species, in terms of the nature and magnitude of noncovalent interactions developed within their monomeric and dimeric forms. In both structures, C-H…O hydrogen bonds are found to be stronger than other noncovalent interactions. Furthermore, H…H bonding contacts and non-conventional C-H…O hydrogen bonds both exhibit a closed shell nature, and play in crucial role in the stability of the novel thiazoles. The isosurfaces in the intermolecular region furnished by NCI molecular diagram signifies the existence of weak noncovalent interactions. Finally, the potential inhibitory activity of the titled compounds and their drug-likeness are demonstrated by molecular docking and ADME-T calculations respectively. Both compounds adhere to the Lipinski's rule of five and present encouraging pharmacokinetic properties and safety profiles.Communicated by Ramaswamy H. Sarma.

Repurposing and computational design of PARP inhibitors as SARS-CoV-2 inhibitors

Coronavirus disease 2019 (COVID-19) is a recent pandemic that caused serious global emergency. To identify new and effective therapeutics, we employed a drug repurposing approach. The poly (ADP ribose) polymerase inhibitors were used for this purpose and were repurposed against the main protease (Mpro) target of severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2). The results from these studies were used to design compounds using the 'Grow Scaffold' modules available on Discovery Studio v2018. The three designed compounds, olaparib 1826 and olaparib 1885, and rucaparib 184 demonstrated better CDOCKER docking scores for Mpro than their parent compounds. Moreover, the compounds adhered to Lipinski's rule of five and demonstrated a synthetic accessibility score of 3.55, 3.63, and 4.30 for olaparib 1826, olaparib 1885, and rucaparib 184, respectively. The short-range Coulombic and Lennard-Jones potentials also support the potential binding of the modified compounds to Mpro. Therefore, we propose these three compounds as novel SARS-CoV-2 inhibitors.

An Integrated Analysis of Mechanistic Insights into Biomolecular Interactions and Molecular Dynamics of Bio-Inspired Cu(II) and Zn(II) Complexes towards DNA/BSA/SARS-CoV-2 3CLpro by Molecular Docking-Based Virtual Screening and FRET Detection

Novel constructed bioactive mixed-ligand complexes (1b) [Cu^II(L)₂(phen)] and (2b) [Zn^II(L)₂(phen)] {where, L = 2-(4-morpholinobenzylideneamino)phenol), phen = 1,10-phenanthroline} have been structurally analysed by various analytical and spectroscopic techniques, including, magnetic moments, thermogravimetric analysis, and X-ray crystallography. Various analytical and spectral measurements assigned showed that all complexes appear to have an octahedral geometry. Agar gel electrophoresis's output demonstrated that the Cu(II) complex (1b) had efficient deoxyribonucleic cleavage and complex (2b) demonstrated the partial cleavage accomplished with an oxidation agent, which generates spreadable OH^● through the Fenton type mechanism. The DNA binding constants observed from viscosity, UV-Vis spectral, fluorometric, and electrochemical titrations were in the following sequence: (1b) > (2b) > (HL), which suggests that the complexes (1b-2b) might intercalate DNA, a possibility that is supported by the biothermodynamic measurements. In addition, the observed binding constant results of BSA by electronic absorption and fluorometric titrations indicate that complex (1b) revealed the best binding efficacy as compared to complex (2b) and free ligand. Interestingly, all compounds are found to interact with BSA through a static approach, as further attested by FRET detection. The DFT and molecular docking calculations were also performed to realize the electronic structure, reactivity, and binding capability of all test samples with CT-DNA, BSA, and the SARS-CoV-2 3CL^Pro, which revealed the binding energies were in a range of -8.1 to -8.9, -7.5 to -10.5 and -6.7--8.8 kcal/mol, respectively. The higher reactivity of the complexes than the free ligand is supported by the FMO theory. Among all the observed data for antioxidant properties against DPPH^᛫, ^᛫OH, O₂^-• and NO^᛫ free radicals, complex (1a) had the best biological efficacy. The antimicrobial and cytotoxic characteristics of all test compounds have been studied by screening against certain selected microorganisms as well as against A549, HepG2, MCF-7, and NHDF cell lines, respectively. The observed findings revealed that the activity enhances coordination as compared to free ligand via Overtone's and Tweedy's chelation mechanisms. This is especially encouraging given that in every case, the experimental findings and theoretical detections were in perfect accord.