1,2-Dibenzoylhydrazine as a Multi-Inhibitor Compound: A Morphological and Docking Study

Xylazine as an emerging new psychoactive substance; focuses on both 5-HT7 and κ-opioid receptors' molecular interactions and isosteric replacement

Xylazine, traditionally used as a veterinary sedative, has recently emerged as a new psychoactive substance, being typically ingested in combination with fentanyl derivatives and hence raising significant public health concerns. Despite its increasing prevalence, little is known about its molecular interactions with human neuroreceptors, specifically the serotonin 7 (5-HT7R) and kappa-opioid (KOR) receptors, which play critical roles in mood regulation, consciousness and nociception. Hence, the binding affinity and molecular interactions of xylazine with both 5-HT7R and KOR through docking simulations and molecular dynamics calculations were investigated. These computational approaches revealed critical insights into receptor binding motifs and highlighted structural modifications that could enhance receptor affinity. The isosteric replacements within the xylazine structure to improve its binding efficacy were assessed, demonstrating that minimal structural modifications can potentiate its interaction with 5-HT7R and KOR. These findings may well advance our understanding of xylazine's mechanism of action, possibly contributing to identifying suitable treatment/management approaches in treating xylazine-related overdoses.

Antiviral efficacy of heparan sulfate and enoxaparin sodium against SARS-CoV-2

As the world transitions from the acute phase of the COVID-19 pandemic caused by SARS-CoV-2, the scientific community continues to explore various therapeutic avenues to control its spread and mitigate its ongoing effects. Among the promising candidates are heparan sulfate (HS) and enoxaparin (EX), which have emerged as potential virus inhibitors. HS, a type of glycosaminoglycan, plays a prominent role in the attachment of the virus to host cells. At the same time, EX, a low-molecular-weight heparin, is being investigated for its ability to disrupt the interaction between the spike protein of SARS-CoV-2 and the ACE2 receptor in human cells. Understanding the mechanisms through which these substances operate could lay the foundation for new strategies in the ongoing management of COVID-19. This study aimed to examine the details of SARS-CoV-2's entry mechanisms and the role of HS in this process. Furthermore, it examines EX's mechanism of action, highlighting how it potentially inhibits SARS-CoV-2. The interactions between HS and the virus, alongside in-vitro and in-silico inhibition studies with HS and EX, are critically analyzed to assess their antiviral efficacy. Additionally, the antiviral activity of sulfated polysaccharides and the potential therapeutic applications of these findings are discussed.

Design, Synthesis, and Evaluation of Novel (-)-cis-N-Normetazocine Derivatives: In Vitro and Molecular Modeling Insights

Suitable structural modifications of the functional groups at N-substituent of (-)-cis-N-normetazocine nucleus modulate the affinity and activity profile of related ligands toward opioid receptors. Our research group has developed several compounds and the most interesting ligands, LP1 and LP2, exhibited a dual-target profile for mu-opioid receptor (MOR) and delta-opioid receptor (DOR). Recent structure-affinity relationship studies led to the discovery of novel LP2 analogs (compounds 1 and 2), which demonstrated high MOR affinity in the nanomolar range. Here, we reported the synthesis of the new (-)-cis-N-normetazocine derivatives (3-8) characterized by the absence of the phenyl ring in the N-substituent compared to all previous reported ligands. Compounds 3 and 4, featuring a methyl ester functional group in the N-substituent, retained significant MOR affinity and exhibited similar affinity for the kappa-opioid receptor (KOR). In contrast, compounds 7 and 8, which contain a hydroxamic acid functionality, maintained affinity exclusively toward MOR. Neither of compounds (3-8) showed DOR affinity. Molecular modeling studies confirmed a similar docking pose in the MOR binding pocket for these compounds. Additionally, the in silico ADME profile of the most interesting ligands (3, 4, 7, and 8) was investigated revealing a favorable profile for compound 7 regarding the blood-brain barrier permeability, suggesting its potential as a peripherally restricted opioid ligand.

Investigating the effect of 1,2-Dibenzoylhydrazine on Staphylococcus aureus using integrated computational approaches

Staphylococcus aureus, a notorious member of the ESKAPE pathogens, poses significant public health challenges due to its virulence and multidrug-resistant nature, particularly in methicillin-resistant S. aureus (MRSA) strains. With the increasing threat of antibiotic resistance, there is an urgent need to develop novel antibiotic agents. This study therefore aims to explore the antibacterial potential of 1,2-dibenzoylhydrazine (DBH) as a scaffold against S. aureus drug target enzymes, using integrated computational approaches. The study utilized molecular docking, lead optimization, and structure-based virtual screening techniques to evaluate the binding affinities of DBH and its derivatives against various S. aureus enzymes. Prime/MM-GBSA calculations were performed to validate the binding affinities obtained, and molecular dynamics (MD) simulations were conducted to assess the stability of the DBHs-enzyme complexes. Results indicated that, out of twenty enzymes from S. aureus examined against DBH, carotenoid dehydrosqualene synthase was predicted as a suitable target enzyme for DBH, showing a binding affinity of -8.027 kcal/mol. A lead optimization operation of the compound generated 27 DBH derivatives out of which four exhibited enhanced binding affinities compared to both DBH and a standard antibiotic, ofloxacin. The QSAR model predicted that, DBH and molecule_D_1 have higher PIC50 of 4.779 µM compared with the standard drug (ofloxacin = 4.678 µM). MD simulations confirmed the stability of the top-scoring derivatives within the enzyme's binding pocket, with RMSD and RMSF analyses supporting their potential as inhibitors of the enzyme. In conclusion, this study has predicted the effect of DBH derivatives on S. aureus based on their in silico inhibitory capacity against the carotenoid dehydrosqualene synthase from the organism. Future work will seek to experimentally validate these findings against the suggested enzyme.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40203-024-00278-1.

THP as a sensor for the electrochemical detection of H2O2

Hydrogen peroxide (H2O2) detection is paramount in biological and clinical domains due to its pivotal role in various physiological and pathological processes. This molecule is a crucial metabolite and effector in cellular redox mechanisms, influencing diverse cellular signaling pathways and bolstering the body's defense mechanisms against infection and oxidative stress. Organic molecule-based electrodes present unique advantages such as operational versatility and scalability, rendering them attractive candidates for sensor development across diverse fields encompassing food safety, healthcare, and environmental monitoring. This study explores the electrochemical properties of a tris(3-hydroxypyridin-4-one) THP, which has been unexplored in electrochemical sensing. Leveraging THP's chelating properties, we aimed to develop an electrochemical probe for hydrogen peroxide detection. Our investigations reveal promising results, with the developed sensor exhibiting a low limit of detection (LOD) of 144 nM, underscoring its potential utility in sensitive and selective H2O2 detection applications. In addition, the new sensor was also tested on fetal bovine serum (FBS) to emphasize future applications on biological matrices. This research signifies a significant stride in advancing electrochemical sensor technologies for hydrogen peroxide detection with several novelties related to the usage of THP, such as high sensitivity and selectivity, performance in biological matrices, repeatability, stability, and reproducibility, economical and practical advantages. This research opens new avenues for enhanced biomedical diagnostics and therapeutic interventions.

γ-Cyclodextrins as Supramolecular Reactors for the Three-component Aza-Darzens Reaction in Water

In recent decades, many efforts have been devoted to studying reactions catalyzed in nanoconfined spaces. The most impressive aspect of catalysis in nanoconfined spaces is that the reactivity of the molecules can be smartly driven to disobey classical behavior. A green and efficient three-component aza-Darzens (TCAD) reaction using a catalytic amount of γ-cyclodextrins (CDs) in water has been developed to synthesize N-phenylaziridines. CDs effectively performed this reaction in an environmentally friendly setting, achieving good yields. The same reaction was then performed using polymeric γ-CD such as a γ-cyclodextrin polymer crosslinked (GCDPC) with epichlorohydrin, a sponge-like macroporous γ-cyclodextrin-based cryogel (GCDC), and a γ-cyclodextrin-based hydrogel (GCDH). The homogeneous and heterogeneous catalyst recovery was then studied, and it was proved to be easily recycled several times without relevant activity loss. Water, as a unique and eco-friendly reaction medium, has been utilized for the first time, to the best of our knowledge, in this reaction. The inclusion of the reagents in CDs has been studied and rationalized by NMR spectroscopy experiments and molecular modeling calculations. The credit of the presented protocol includes good yields and catalyst reusability and precludes the use of organic solvents.

Discovery of first novel sigma/HDACi dual-ligands with a potent in vitro antiproliferative activity

Designing and discovering compounds for dual-target inhibitors is challenging to synthesize new, safer, and more efficient drugs than single-target drugs, especially to treat multifactorial diseases such as cancer. The simultaneous regulation of multiple targets might represent an alternative synthetic approach to optimize patient compliance and tolerance, minimizing the risk of target-based drug resistance due to the modulation of a few targets. To this end, we conceived for the first time the design and synthesis of dual-ligands σR/HDACi to evaluate possible employment as innovative candidates to address this complex disease. Among all synthesized compounds screened for several tumoral cell lines, compound 6 (Kiσ1R = 38 ± 3.7; Kiσ2R = 2917 ± 769 and HDACs IC50 = 0.59 µM) is the most promising candidate as an antiproliferative agent with an IC50 of 0.9 µM on the HCT116 cell line and no significant toxicity to normal cells. Studies of molecular docking, which confirmed the affinity over σ1R and a pan-HDACs inhibitory behavior, support a possible balanced affinity and activity between both targets.

Progress of the "Molecular Informatics" Section in 2022

This is the first Editorial of the "Molecular Informatics" Section (MIS) of the International Journal of Molecular Sciences (IJMS), which was created towards the end of 2018 (the first article was submitted on 27 September 2018) and has experienced significant growth from 2018 to now [...].

Selective noncovalent proteasome inhibiting activity of trifluoromethyl-containing gem-quaternary aziridines

The ubiquitin-proteasome pathway (UPP) represents the principal proteolytic apparatus in the cytosol and nucleus of all eukaryotic cells. Nowadays, proteasome inhibitors (PIs) are well-known as anticancer agents. However, although three of them have been approved by the US Food and Drug Administration (FDA) for treating multiple myeloma and mantel cell lymphoma, they present several side effects and develop resistance. For these reasons, the development of new PIs with better pharmacological characteristics is needed. Recently, noncovalent inhibitors have gained much attention since they are less toxic as compared with covalent ones, providing an alternative mechanism for solid tumors. Herein, we describe a new class of bis-homologated chloromethyl(trifluoromethyl)aziridines as selective noncovalent PIs. In silico and in vitro studies were conducted to elucidate the mechanism of action of such compounds. Human gastrointestinal absorption (HIA) and blood-brain barrier (BBB) penetration were also considered together with absorption, distribution, metabolism, and excretion (ADMET) predictions.

Steered Molecular Dynamics Simulations Study on FABP4 Inhibitors

Ordinary small molecule de novo drug design is time-consuming and expensive. Recently, computational tools were employed and proved their efficacy in accelerating the overall drug design process. Molecular dynamics (MD) simulations and a derivative of MD, steered molecular dynamics (SMD), turned out to be promising rational drug design tools. In this paper, we report the first application of SMD to evaluate the binding properties of small molecules toward FABP4, considering our recent interest in inhibiting fatty acid binding protein 4 (FABP4). FABP4 inhibitors (FABP4is) are small molecules of therapeutic interest, and ongoing clinical studies indicate that they are promising for treating cancer and other diseases such as metabolic syndrome and diabetes.

Design, synthesis, in vitro evaluation, and molecular modeling studies of N-substituted benzomorphans, analogs of LP2, as novel MOR ligands

6,7-Benzomorphans have been investigated in medicinal chemistry for developing new drugs. This nucleus could be considered a versatile scaffold. The physicochemical properties of benzomorphan N-substituent are crucial in achieving a definite pharmacological profile at opioid receptors. Thus, the dual-target MOR/DOR ligands LP1 and LP2 were obtained through N-substituent modifications. Specifically, LP2, bearing as N-substituent the (2R/S)-2-methoxy-2- phenylethyl group, is a dual-target MOR/DOR agonist and is successful in animal models of inflammatory and neuropathic pain. To obtain new opioid ligands, we focused on the design and synthesis of LP2 analogs. First, the 2-methoxyl group of LP2 was replaced by an ester or acid functional group. Then, spacers of different lengths were introduced at N-substituent. In-vitro, their affinity profile versus opioid receptors has been performed through competition binding assays. Molecular modeling studies were conducted to deeply analyze the binding mode and the interactions between the new ligands and all opioid receptors.