Chemical modifications of a compound-of-interest, such as an enzyme inhibitor, are at the basis of performing robust structure-activity relationships able to address synthetic efforts toward more and more potent ligands. In this context, substitution patterns on phenyl rings, e.g., introduction of electron-donor/withdrawing groups, are widely explored. Generation of derivatives is based on different approaches, including molecular modeling, the emerging artificial intelligence, or the more traditional organic chemistry strategy. The latter usually follows practical guidelines, e.g., the Topliss scheme, or the actual laboratory availability of chemicals. In the last decade, Prof. La Motta’s group has been involved in the development of new anticancer agents targeting Aldehyde Dehydrogenases (ALDHs, EC: 1.2.1.3), enzymes involved in the detoxifying conversion of aldehydes into the safer corresponding carboxylic acids, recognized as Cancer Stem Cells biomarkers and overexpressed in solid tumors. Derivatives libraries containing the imidazo[1,2-a]pyridine scaffold have been proposed as ALDH inhibitors and isoform selectivity has been reached through different phenyl substitution patterns. In particular, a potent and selective ALDH1A3 inhibitor (3q, IC₅₀ = 3.5 µM) endowed with three methoxy substituents in specific phenyl positions was previously reported. Thus, we enlarged the derivatives series of 3q, also synthesizing its corresponding demethylated derivative (1). Unexpectedly, a complete loss of inhibitory activity was observed for 1, still possessing a promising antiproliferative effect on a thyroid primary cell line. In silico analyses on ALDHs were performed to elucidate why such a small chemical modification severely affected the activity. Then, we investigated the actual antiproliferative mechanism of action of 1 by exploring in wet different possibilities, e.g., kinases and carbonic anhydrases, providing partial but interesting information.

Some of the most used chemotherapeutic agents in oncological therapies are derived from natural substances, in particular from plants. These compounds can be extracted from various parts of plants, such as roots, leaves, flowers, or fruits, and are often recognized for their anti-cancer or antitumor properties. Some well-known examples of plant-derived chemotherapeutics include: Taxol extracted from the Pacific yew tree (Taxus brevifolia Nutt.) and another taxanes obtained from Taxus baccata L., Camptothecin extracted from happy tree (Camptotheca acuminata Decne.), Vinblastine and Vincristine extracted from the periwinkle plant (Catharanthus roseus (L.) G.Don) and more. In this study, the anti-leukemic activity of a plant widely distributed in Sardinia, the second-largest Italian island in the Mediterranean Sea, Vinca sardoa (Stearn) Pignatti, known as Sardinian periwinkle, was investigated. This species is known for its indole alkaloids, which exhibit a wide range of biological activities. Three extracts obtained from the aerial parts of plants cultivated in Italy, two from Iglesias (Sardinia) and one from Rome (Italy), were tested at different concentrations (1, 5, 10, and 15 mg/mL) on a B lymphoblast cell line (SUP-B15). Each extract demonstrated a good capacity to induce reductions in cell proliferation of up to 50%, and none of the concentrations exhibited cytotoxicity on normal cells.

Antimicrobial peptides (AMPs) have emerged as a novel class of anti-infectives to combat microbial resistance. However, their intrinsic characteristics, including low target affinity and limited in vivo stability, present obstacles to their therapeutic development. Macrocyclic peptides, a diverse peptide family, offer improved metabolic and proteolytic stability along with high target affinity. In this work, we performed an analysis of the DBAASP database to enhance our understanding of small cyclic peptides, nature’s defense mechanisms for living organisms. To our knowledge, this is the first effort to characterize cyclic peptides originated from either non-ribosomal or post-ribosomal peptide synthesis and reveal shared and distinctive cyclization patterns. The Database of Antimicrobial Activity and Structure of Peptides (DBAASP) provides invaluable data on structural characteristics and experimental testing of AMPs, encompassing over 4,400 cyclic AMPs. Natural peptides within DBAASP are categorized based on their synthesis type: ribosomal and non-ribosomal. Currently, DBAASP contains 1346 ribosomal and 475 non-ribosomal cyclic AMPs. We conducted an analysis of this dataset, considering peptide length, amino acid composition, intrachain bonding for cyclization, and mechanisms of action. The methods of cyclization, types of cycles, and their peculiarities in the composition of small cyclic peptides have also been explored. Analysing this wealth of information not only deepens our understanding of cyclic AMPs but also inspires strategies for designing novel AMPs with enhanced therapeutic potential.

The aquaporins 3 (AQP3) are tetrameric membrane-bound channels that facilitate transport of water and other small solutes across skin cell membranes. The recent findings revealed that AQP3 are involved in the progression of skin disorders, such as atopic dermatitis, psoriasis, eczema, vitiligo, and xerosis. Research of novel combination of plant molecules that could increase the expression of this protein for skin hydration is currently ongoing. Through DiffDock computational modelling to predict affinity for AQP3 and the biological activity, Aloe vera extract and trimethylglycine were chosen. Thus, our science work was focused on the development of a novel combination based on Aloe vera extract and trimethylglycine and evaluation of targeted AQP3 regulation in skin keratinocytes in the presence of this combination. Firstly, the cytotoxicity assay of selected substances was performed with MTT indicator on HaCaT cells. Secondly, the substances’ ability to increase amount of AQP3 was evaluated in the keratinocytes’ cell culture with ELISA immunoassay. According to the results obtained, the novel combination based on Aloe vera extract and trimethylglycine in a mass ratio of 1:1 had a good cytotoxicity profile, with an EC70 value of 11.95%. Moreover, it was shown that the combination had a clear synergetic activity and significantly increased amount of epidermal AQP3 up to 219%, compared to that of negative control (p<0.001). Thus, the novel combination of plant molecules has a promising potential for the development of dermatological drugs and the treatment of skin disorders related to the low skin hydration.

Bacteria within biofilms display remarkable antibiotic resistance compared to planktonic bacteria. Given their implications in infectious diseases and multidrug resistance, exploring effective antimicrobial strategies to regulate biofilm formation is urgent. Eradicating bacteria within biofilms is challenging, needing combination therapy to combat persistent biofilm-related infections. In previous studies, we demonstrated the synergistic and partially synergistic effects of Ciprofloxacin (CIP) combined with antibacterial sulfonamides (SA) against Escherichia coli reference and clinical strains with intermediate quinolone resistance (E. coli IRQ). Notably, the CIP+ sulfadiazine (SDZ) combination exhibited superior efficacy. In this study, we assessed the antibiofilm activity of CIP and SDZ combinations on mature biofilms formed on glass discs using scanning electron microscopy (SEM), focusing on the E. coli IRQ strain. Mature biofilms (48-hour growth) were treated with individual antibiotics (CIP and SDZ) and their combinations (CIP+SDZ), considering minimal fractional inhibitory concentrations (FIC) from previous studies. The experiment was performed in triplicate. Treatments included: CIP (FICx100) + SDZ (FICx10), CIP (FICx100), and SDZ (FICx10). SEM micrographs highlighted an enhanced antibiofilm effect of CIP+SDZ combinations compared to individual drugs. Specifically, CIP (FICx100) + SDZ (FICx10) significantly reduced biofilm formation, caused disorganization, reduced extracellular matrix, and induced bacterial cell destruction, outperforming untreated and individually treated biofilms. These findings provide insights into the partially synergistic effect of this combination on E. coli IRQ, attributed to cooperative actions targeting diverse stages of DNA synthesis. The study underscores CIP+SDZ as a promising combination for treating biofilm-related infections.

The Proteasome is a multi-catalytic enzyme complex found in the nucleus and cytoplasm of all eukaryotic cells. It is the primary intracellular proteolytic system involved in intracellular proteolysis. The ubiquitin-proteasome pathway is essential for the regulated degradation of intracellular proteins in eukaryotic cells. So, proteasome inhibition is a targeted therapy for cancer to promote cell cycle arrest or apoptosis. Bortezomib is the first selective proteasome inhibitor for treating multiple myeloma. But bortezomib displays severe side effects due to non-specific cytotoxicity towards healthy tissue. So, there is a clear need to develop new proteasome inhibitors with improved safety and efficacy profiles. In this research, we have developed a tripeptide vinyl sulfone based on azobenzene for proteasome inhibition studies. These proteasome inhibitors exhibit photo-switchable activity upon exposure to 365nm light irradiation. The photo-conversion from trans to cis configuration exceeded 90%, as verified by HPLC and proton NMR studies. After confirming the photoisomerization of our synthesized molecules, we conducted theoretical docking studies to assess the binding affinity of those molecules within the proteasome's active site. Subsequent proteasome inhibition assays demonstrated that cis-enriched isomers exhibited greater potency compared to their trans counterparts. Further investigation involved evaluating cell viability in various cancer cell lines, including A549, Hela, and MCF7, consistently revealing that cis isomers of the azobenzene compounds were more cytotoxic. Notably, our most potent compound displayed a nearly tenfold difference in activity between its trans and cis isomers across these cancer cell lines, which translating the proteasome inhibition into cancer cells.

Keywords

Proteasome inhibitors; Protein degradation pathway; sulfone based proteasome inhibitors; azobenzene; photo-switchable inhibitors; spatiotemporal control; cis-trans isomerization; proteasome beta-5 inhibition; cellular toxicity; cell viability in different cancer cell

AUTHORS INFORMATION

Corresponding Author

*Pakkirisamy Thilagar, Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, India - 560012

Email: thilagar@iisc.ac.in

Author contributions

These authors contributed in the sequence as mentioned.

Institutional Review Board Statement

Not applicable

Information Consent Statement

Not applicable

Conflicts of Interest

The authors declare no conflict of interest.

Acknowledgement

Authors thankful to IISc Bangalore, DST and SERB for financial support. SS , SP and PT thanks to CSIR, IISc Bangalore.

This study aimed to implement the Junction Tree Variational autoencoder (JT-VAE) in conjunction with a gradient ascent algorithm to explore the chemical space of potential inhibitors of Histone deacetylase 6 (HDAC6). In the generation stage, a diverse subset of active compounds was identified using the Butina algorithm. These compounds were then subjected to chemical space exploration employing JT-VAE and a gradient ascent algorithm. The generated substances were subsequently reassessed using an Artificial neural networks model and molecular docking (PDB ID: 6CE6) studies. Thirty-one active compounds with a Tanimoto coefficient under 0.35 were identified from 5225 compounds collected from the ChEMBL database. These compounds underwent a chemical exploration stage, resulting in the generation of 303 novel substances. An artificial neural network-based quantitative structure-activity relationship (ANN-QSAR) model was constructed to predict the inhibitory values of these generated compounds, with external validation yielding an R2 value of 0.595 and an RMSE value of 0.643. Subsequently, a retrospective control protocol was used to determine the scoring function and the cutoff of binding affinity energy, using Deepcoys to generate decoys without bias at a ratio of 1:50 (active:decoys) through deep learning algorithm. Finally, Vinardo was chosen as the preferred scoring function in the GNINA software due to its superior ROC-AUC value of 0.715 when compared to two other scoring functions, and 13 distinguished compounds were identified with a pChEMBL Value threshold above 7 and binding affinity below -7.69 kcal/mol, representing a significant advancement in the field of HDAC6 inhibitor discovery. This multi-pronged approach efficiently identified potential inhibitors of Histone deacetylase 6 (HDAC6), suggesting the following stages involve synthesis and biological testing.

Soursop plant, (Annona muricata) which is indigenous to the tropics belongs to the family Annonaceae. Parts of the plant has been used in traditional medicine to cure several diseases. The physiological, physicochemical and nutritional characteristics of soursop plant has been reported in several studies, alongside the presence of bioactive compounds in the pulp, seed, columella and peel. Prostate cancer is the most cancer diagnosis in men and is still the third-leading cause of cancer related death in males.

Bioactive compounds isolated from the pulp have demonstrated cytotoxic activity against human prostate cancer cells, as reported by several studies. Amongst which seven were selected for the purpose of this study. This study employed in silico method to provide insight into the binding affinity of some bioactive compounds present in soursop pulp as compared to native ligand present in the target enzymes Androgen Receptor (AR) and primary poly (ADP-ribose) polymerase (PARP) with PDB (Protein Data Bank) codes, 2HYD and 7ONS respectively.

The results from this study, showed that all the chosen bioactive compounds had comparable binding activity to the native ligand with the exception of annonacin. These findings could give insights into the development of new pharmaceutical drugs with more cytotoxic effect against prostate cancer or even serve as alternate method for treating prostate cancer.

Fungi have received much attention as a source of bioactive compounds with variety of therapeutic properties such as antioxidant, antibacterial, antiviral, antiparasitic and anticancer activities. With great biomedical potential, these pharmacologically-active natural products tend to replace the currently used synthetic drugs. The objective of this study was to evaluate the antioxidant potential, aldo-keto reductase (AKR) inhibition, and estrogen receptor binding affinity of two different extract types (70% ethanolic and hot water) derived from one indigenous fungal species, namely Fomes fomentarius sampled from Uzbekistan.

Evaluation of antioxidant activity in the tested fungal extracts was conducted using established in vitro assays, including ABTS, DPPH, and FRAP. Fungal extracts were tested in vitro for binding affinity to ligand-binding domains of estrogen receptor α and estrogen receptor β using fluorescencent screen in yeast and their potential to inhibit aldo-keto reductases, valuable targets for the treatment of hormone-dependent diseases. The results revealed that the highest scavenging activity and reducing power potential was observed for the analyzed 70% EtOH extract (DPPH: 12.11 mg TE/g d.w., ABTS: 124.24 mg TA/g d.w. and FRAP: 350.52 mg TE/g d.w.).

Similarly, the 70% EtOH extract of F. fomentarius exhibited higher inhibition potential against AKR1C3 (91.9%) than the hot water extract (35.7%). These fungal extracts showed weak inhibition against AKR1C4 isoform and no estrogenicity, making them promising candidates for the design of anticancer therapeutics against estrogen-dependent breast cancer.

In conclusion, our study highlights the promising potential of F. fomentarius extracts as a basis for additional study in the searching for novel natural anticancer drugs.

Nicotinonitriles, nicotinamides and their partially saturated analogs represent a promising class of heterocyclic compounds with an interesting range of biological activities. One of the most accessible and efficient approaches to the synthesis of functionalized nicotinamides is based on the reaction of active methylene malonamides with 1,3- dielectrophiles. Synthesized compounds were subjected to virtual screening using GalaxySagittarius and SwissTargetPrediction services which led to the discovery of FXIa inhibition activity in one of the compounds. In order to validate the result of virtual screening pharmacophore analysis was produced with Molecular Operating Environment software. Moreover, structural approach well known as molecular docking and the most promising method in silico was used with Molegro Virtual Docker. As a target for docking was chosen FXIa (7MBO) in a complex with milvexian. After proper protein preparing interaction of a ligand and a biotarget was evaluated with scoring-functions MolDockScore and HBond. According to ADMET data obtained after virtual assessment the hit-compound is supposed to be soluble, well absorbed in gastrointestinal tract and non-carcinogenic. The results of in silico studies allow to represent the ligand as a perspective platform for further FXIa high-selective inhibitor development.