In silico approach: docking study of oxindole derivatives against the main protease of COVID-19 and its comparison with existing therapeutic agents

Comprehensive assessment of 3-benzyloxyflavones as β-glucosidase inhibitors: in vitro, in vivo, kinetic, SAR and computational studies

In this study, a series of 3-benzyloxyflavone derivatives (1-10) was designed and, for the first time, evaluated for both in vitro and in vivo inhibitory activity against the β-glucosidase enzyme. The enzyme inhibitory potential of these derivatives was further assessed in an antihyperglycemic context using in vivo mechanism-based assays on p-nitrophenyl-β-d-glucopyranoside (PGLT) induced diabetic models. Additionally, structure-activity relationship (SAR) was employed to identify structural features crucial for activity. Molecular docking analyses revealed that both the potent compounds and co-crystallized ligands shared similar binding orientations within the active sites of β-glucosidase (PDB IDs: 3AJ7; 66K1). Molecular dynamics (MD) simulations validated the stability of the inhibitor-enzyme complexes under physiological conditions, while density functional theory (DFT) calculations helped elucidate electronic properties critical for activity. Drug-likeness analysis was also conducted to assess the pharmacokinetic potential of the derivatives. The results highlighted several derivatives with significant inhibitory activity, desirable pharmacokinetic profiles, and promising drug-like properties, making them potential candidates for therapeutic development. The target derivatives (1-10) demonstrated strong potential as lead compounds for developing new anti-diabetic agents with effective anti-hyperglycemic properties.

Pharmacological evaluation of 3-benzyloxyflavones for β-glucosidase inhibition: Experimental, kinetic and computational approaches

β-Glucosidase is a crucial enzyme involved in carbohydrate metabolism, playing a key role in the hydrolysis of glycosidic bonds in dietary polysaccharides. Inhibition of β-glucosidase has emerged as a promising therapeutic strategy for managing postprandial hyperglycemia in diabetes by delaying/slowing glucose absorption and moderating blood sugar levels. In this study, a series of 3-benzyloxyflavone derivatives (1-10) was designed and, for the first time, evaluated for both in vitro and in vivo inhibitory activity against the β-glucosidase enzyme. The enzyme inhibitory potential of these derivatives was further assessed in an antihyperglycemic context using in vivo mechanism-based assays on p-nitrophenyl-β-D-glucopyranoside (PGLT) induced diabetic models. Additionally, structure-activity relationship (SAR) was employed to identify structural features crucial for activity. Molecular docking analyses revealed that both the potent compounds and co-crystallized ligands shared similar binding orientations within the active sites of β-glucosidase (PDB IDs: 3AJ7; 66K1). Molecular dynamics (MD) simulations validated the stability of the inhibitor-enzyme complexes under physiological conditions. Drug-likeness analysis was also conducted to assess the pharmacokinetic potential of the derivatives. We have also conducted Density Functional Theory (DFT) studies on the lead compounds to gain deeper insights into their electronic properties, structural stability, and interaction mechanisms with the target enzyme. The results highlighted several derivatives with significant inhibitory activity, desirable pharmacokinetic profiles, and promising drug-like properties, making them potential candidates for therapeutic development. The target derivatives (1-10) demonstrated strong potential as lead compounds for developing new anti-diabetic agents with effective anti-hyperglycemic properties.

Macromolecular interaction mechanism of the bacteriocin EntDD14 with the receptor binding domain (RBD) for the inhibition of SARS-CoV-2 and the JN.1 variant: Biomedical study based on elastic networks, stochastic Markov models, and macromolecular volumetric analysis

Bacteriocins, a class of molecules produced by bacteria, exhibit potent antimicrobial properties, including antiviral activities. The urgent need for treatments against SARS-CoV-2 has proposed bacteriocins such as enterocin DD14 (EntDD14) as potential therapeutic agents. However, the mechanism of macromolecular interaction of EntDD14 for the inhibition of SARS-CoV-2 is not yet fully understood, and its efficacy against variants like JN.1 has not been completely established. To address these knowledge gaps, biocomputational analyses were employed using a diverse set of tools, including Markov state models and volumetric analyses. This analysis revealed a favorable interaction between EntDD14 and the receptor-binding domain (RBD) of SARS-CoV-2. Furthermore, it was found that EntDD14 induces changes in the flexibility of the RBD and alters the distribution and size of its internal cavities, particularly in the JN.1 variant. These findings align with experimental observations and support the inhibitory mechanism of EntDD14 against SARS-CoV-2. Additionally, they suggest that EntDD14 may possess a broader spectrum of action, encompassing the JN.1 variant. This study paves the way for future investigations and therapeutic applications, encouraging further exploration of the antiviral activity of bacteriocins like EntDD14 against variants of concern like JN.1. However, additional experimental demonstrations are warranted to substantiate these findings.

A virtual insight into mushroom secondary metabolites: 3D-QSAR, docking, pharmacophore-based analysis and molecular modeling to analyze their anti-breast cancer potential

Breast cancer is a major issue of investigation in drug discovery due to its rising frequency and global dominance. Plants are significant natural sources for the development of novel medications and therapies. Medicinal mushrooms have many biological response modifiers and are used for the treatment of many physical illnesses. In this research, a database of 89 macro-molecules with anti-breast cancer activity, which were previously isolated from the mushrooms in literature, has been selected for the three-dimensional quantitative structure-activity relationships (3D-QSAR) studies. The 3D-QSAR model was necessarily used in Pharmacopoeia virtual evaluation of the database to develop novel MCF-7 inhibitors. With the known potential targets of breast cancer, the docking studies were achieved. Using molecular dynamics simulations, the targets' stability with the best-chosen natural product molecule was found. Furthermore, the absorption, distribution, metabolism, excretion, and toxicity of three compounds, resulting after the docking study, were predicted. The compound C1 (Pseudonocardian A) showed the features of effective compounds because it has bioavailability from different coral species and is toxicity-free for the prevention of many dermatological illnesses. C1 is chemically active and possesses charge transfer inside the monomer, as seen by the band gaps of highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) electrons. The reactivity descriptors ionization potential, electron affinity, chemical potential (μ), hardness (η), softness (S), electronegativity (χ), and electrophilicity index (ω) have been estimated using the energies of frontier molecular orbitals (HOMO-LUMO). Additionally, molecular electrostatic potential maps were created to show that the C1 is reactive.Communicated by Ramaswamy H. Sarma.

The Discovery of Novel Small Oxindole-Based Inhibitors Targeting the SARS-CoV-2 Main Protease (Mpro )

With the potential for coronaviruses to re-emerge and trigger future pandemics, the urgent development of antiviral inhibitors against SARS-CoV-2 is essential. The Mpro enzyme is crucial for disease progression and the virus's life cycle. It possesses allosteric sites that can hinder its catalytic activity, with some of these sites located at or near the dimerization interface. Among them, sites #2 and #5 possess druggable pockets and are predicted to bind drug-like molecules. Consequently, a commercially available ligand library containing ~7 million ligands was used to target site #2 via structure-based virtual screening. After extensive filtering, docking, and post-docking analyses, 53 compounds were chosen for biological testing. An oxindole derivative was identified as a Mpro non-competitive reversible inhibitor with a Ki of 115 μM and an IC50 of 101.9 μM. Throughout the 200 ns-long MD trajectories, our top hit has shown a very stable binding mode, forming several interactions with residues in sites #2 and #5. Moreover, derivatives of our top hit were acquired for biological testing to gain deeper insights into their structure-activity relationship. To sum up, drug-like allosteric inhibitors seem promising and can provide us with an additional weapon in our war against the recent pandemic, and possibly other coronaviruses-caused diseases.

Indole-Based Compounds as Potential Drug Candidates for SARS-CoV-2

The COVID-19 pandemic has posed a significant threat to society in recent times, endangering human health, life, and economic well-being. The disease quickly spreads due to the highly infectious SARS-CoV-2 virus, which has undergone numerous mutations. Despite intense research efforts by the scientific community since its emergence in 2019, no effective therapeutics have been discovered yet. While some repurposed drugs have been used to control the global outbreak and save lives, none have proven universally effective, particularly for severely infected patients. Although the spread of the disease is generally under control, anti-SARS-CoV-2 agents are still needed to combat current and future infections. This study reviews some of the most promising repurposed drugs containing indolyl heterocycle, which is an essential scaffold of many alkaloids with diverse bio-properties in various biological fields. The study also discusses natural and synthetic indole-containing compounds with anti-SARS-CoV-2 properties and computer-aided drug design (in silico studies) for optimizing anti-SARS-CoV-2 hits/leads.

Design, Synthesis and In Vitro Evaluation of Spirooxindole-Based Phenylsulfonyl Moiety as a Candidate Anti-SAR-CoV-2 and MERS-CoV-2 with the Implementation of Combination Studies

The search for an effective anti-viral to inhibit COVID-19 is a challenge for the specialized scientific research community. This work investigated the anti-coronavirus activity for spirooxindole-based phenylsulfone cycloadducts in a single and combination protocols. The newly designed anti-SARS-CoV-2 therapeutics spirooxindoles synthesized by [3 + 2] cycloaddition reactions represent an efficient approach. One-pot multicomponent reactions between phenyl vinyl sulfone, substituted isatins, and amines afforded highly stereoselective anti-SARS-CoV-2 therapeutics spirooxindoles with three stereogenic centers. Herein, the newly synthesized spirooxindoles were assessed individually against the highly pathogenic human coronaviruses and proved to be highly potent and safer. Interestingly, the synergistic effect by combining the potent, tested spirooxindoles resulted in an improved antiviral activity as well as better host-cell safety. Compounds 4i and 4d represented the most potent activity against MERS-CoV with IC₅₀ values of 11 and 23 µM, respectively. Both compounds 4c and 4e showed equipotent activity with the best IC₅₀ against SARS-CoV-2 with values of 17 and 18 µM, respectively, then compounds 4d and 4k with IC₅₀ values of 24 and 27 µM, respectively. Then, our attention oriented to perform a combination protocol as anti-SARS-CoV-2 for the best compounds with a different binding mode and accompanied with different pharmacophores. Combination of compound 4k with 4c and combination of compounds 4k with 4i proved to be more active and safer. Compounds 4k with 4i displayed IC₅₀ = 3.275 µM and half maximal cytotoxic-concentration CC₅₀ = 11832 µM. MD simulation of the most potential compounds as well as in silico ADMET properties were investigated. This study highlights the potential drug-like properties of spirooxindoles as a cocktail anti-coronavirus protocol.

Inhibition of Mycobacterium tuberculosis InhA (Enoyl-acyl carrier protein reductase) by synthetic Chalcones: a molecular modelling analysis and in-vitro evidence

Tuberculosis (TB) is a serious infectious disease caused by the bacillus Mycobacterium tuberculosis (Mtb). The World Health Organization (WHO) estimates that 1.8 million people die each year from TB, with 10 million new cases being registered each year. In this study, 50 Chalcones were developed, five of which were synthesized, and their inhibitory effects against Mtb were studied. The discovery of new powerful inhibitors with IC₅₀ values in the sub-micro molar range resulted from the development of structure-activity relationships (SAR). The goal of the molecular modelling studies was to uncover the most important structural criteria underpinning the binding affinity and selectivity of this class of inhibitors as possible anti-TB drugs. Because of their great efficacy and selectivity, our developed nitro and benzyloxy substituted Chalcones compounds appear to be promising anti-TB therapies.Communicated by Ramaswamy H. Sarma.

In silico docking and ADME study of deketene curcumin derivatives (DKC) as an aromatase inhibitor or antagonist to the estrogen-alpha positive receptor (Erα+): potent application of breast cancer

Regardless of many extensive studies, hormonal-based breast cancer is the most common cause of cancer-related mortality of females worldwide. Indeed, estrogen receptor-positive (ER +) is the communal subtype in breast cancer. To treat this, three types of medications are typically used: selective estrogen receptor modulators (SERMs), selective estrogen receptor down modulators (SERDMs), and aromatase inhibitors (AIs), all of which directly interact with the activation of the estrogen signaling pathway and its formation. Despite their effectiveness, the development of new treatments is required since clinical efficacy is restricted owing to resistance. As a result, in silico studies for drug discovery are booming over the decades because of their affordability and less time-consuming features. Here, 25 deketene curcumin derivatives have been selected for docking studies through MVD software over the positive type of breast cancer through both the treatment hosts Erα + receptor and aromatase. DKC compounds are used because they have several pharmacological uses, including anti-cancer, anti-diabetic, anti-viral, anti-fungal, and anti-bacterial properties. Moreover, an ADME study was carried out for DKC derivatives that reveal the optimum drug-likeness profile. From 25 derivatives, the results showed a better MolDock score, hydrogen bonding, and steric interaction between compounds DKC-10, DKC-20, and DKC-21 with Erα + and aromatase. Although the study was done on both the treatable path hosts, better results were obtained with Erα + as an antagonist. Therefore, it is proposed that three selected DKC derivatives would be better therapeutic agents against breast cancer.