Synthesis, anticancer, structural, and computational docking studies of 3-benzylchroman-4-one derivatives

Synthesis, molecular docking studies and biological evaluation of N-(4-oxo-2-(trifluoromethyl)-4H-chromen-7-yl) benzamides as potential antioxidant, and anticancer agents

A series of novel chromone derivatives of (N-(4-oxo-2-(trifluoromethyl)-4H-chromen-6-yl) benzamides) were synthesized by treating 7-amino-2-(trifluoromethyl)-4H-chromen-4-one with K2CO3 and/or NaH, suitable alkyl halides and acetonitrile and/or 1,4-dioxane. The obtained products are in high yields (87 to 96%) with various substituents in short reaction times with no more by-products and confirmed by FT-IR, 1H, and 13C-NMR Spectral data. The in vitro cytotoxic activity was examined against two human cancer cell lines, namely the human lung adenocarcinoma (A-549) and the human breast (MCF-7) cancer cell line. Compound 4h showed promising cytotoxicity against both cell lines with IC50 values of 22.09 and 6.40 ± 0.26 µg/mL respectively, compared to that of the standard drug. We also performed the in vitro antioxidant activity by DPPH radical, hydrogen peroxide, NO scavenging, and total antioxidant capacity (TAC) assay methods, and they showed significant activities. The possible binding interactions of all the synthesized chromone derivatives are also investigated against selective pharmacological targets of human beings, such as HERA protein for cytotoxic activity and Peroxiredoxins (3MNG) for antioxidant activity which showed closer binding free energies than the standard drugs and evidencing the above two types of activities.

Chromanone-A Prerogative Therapeutic Scaffold: An Overview

Chromanone or Chroman-4-one is the most important and interesting heterobicyclic compound and acts as a building block in medicinal chemistry for isolation, designing and synthesis of novel lead compounds. Structurally, absence of a double bond in chromanone between C-2 and C-3 shows a minor difference from chromone but exhibits significant variations in biological activities. In the present review, various studies published on synthesis, pharmacological evaluation on chroman-4-one analogues are addressed to signify the importance of chromanone as a versatile scaffold exhibiting a wide range of pharmacological activities. But, due to poor yield in the case of chemical synthesis and expensive isolation procedure from natural compounds, more studies are required to provide the most effective and cost-effective methods to synthesize novel chromanone analogs to give leads to chemistry community. Considering the versatility of chromanone, this review is designed to impart comprehensive, critical and authoritative information about chromanone template in drug designing and development.

New chromanone derivatives containing thiazoles: Synthesis and antitumor activity evaluation on A549 lung cancer cell line

Novel 2-[2-(chroman-4-ylidene)hydrazinyl]-4/5-substituted thiazole derivatives (2a-i) were synthesized and investigated for their anticancer activity. Cytotoxic activity on A549 and NIH/3T3 cell lines was determined, most of the compounds exhibited high cytotoxic profile with selectivity. Selected compounds 2b, 2c, 2e, 2g, 2h, and 2i were tested to determine induction of apoptosis, mitochondrial membrane depolarization, and cell cycle arrest. The results showed that the compounds induced apoptosis intrinsically that they triggered loss of mitochondrial potential through increasing the accumulation of cells in G2/M. Besides, intrinsic apoptotic pathway was supported by down-regulation of anti-apoptotic protein Bcl-2 and up-regulation of proapoptotic protein Bax. Molecular docking study for compounds 2b, 2c, and 2g was promoted experimental outcomes.

Unraveling the Allosteric Mechanism of Four Cancer-related Mutations in the Disruption of p53-DNA Interaction

The p53 protein plays active roles in the physiological regulation of cell cycle as well as in cancer developments. In more than half of human cancers, the protein is inactivated by mutations located primarily in its DNA-binding domain (DBD), and some mutations located in the β-sandwich region of DBD are reported to decrease p53-DNA binding affinities. To understand the long-range correlation between p53 β-sandwich and DNA, and the allosteric mechanism of β-sandwich mutations in the disruption of p53-DNA interactions, we first identify three regions with a strong correlation with DNA based on microsecond molecular dynamics (MD) simulations of wild-type p53-DNA complex and then perform multiple MD simulations on four cancer-related mutants L145Q, P151S, Y220C, and G266R, which are located in these three regions. Our simulations show that these mutations allosterically destabilize the structural stability of the DNA-binding groove in p53 and disrupt the p53-DNA interactions. Network analyses reveal optimal correlation paths through which the mutation-induced allosteric signal passes to DNA, and the disturbance effect of these mutations on the global connectivity and dynamical correlation of the p53-DNA complex. This work paves the way for the in-depth understanding of the mutation-induced loss in p53's DNA-recognition ability and the pathological mechanism of cancer development.

SANCDB: an update on South African natural compounds and their readily available analogs

BACKGROUND

South African Natural Compounds Database (SANCDB; https://sancdb.rubi.ru.ac.za/ ) is the sole and a fully referenced database of natural chemical compounds of South African biodiversity. It is freely available, and since its inception in 2015, the database has become an important resource to several studies. Its content has been: used as training data for machine learning models; incorporated to larger databases; and utilized in drug discovery studies for hit identifications.

DESCRIPTION

Here, we report the updated version of SANCDB. The new version includes 412 additional compounds that have been reported since 2015, giving a total of 1012 compounds in the database. Further, although natural products (NPs) are an important source of unique scaffolds, they have a major drawback due to their complex structure resulting in low synthetic feasibility in the laboratory. With this in mind, SANCDB is, now, updated to provide direct links to commercially available analogs from two major chemical databases namely Mcule and MolPort. To our knowledge, this feature is not available in other NP databases. Additionally, for easier access to information by users, the database and website interface were updated. The compounds are now downloadable in many different chemical formats.

CONCLUSIONS

The drug discovery process relies heavily on NPs due to their unique chemical organization. This has inspired the establishment of numerous NP chemical databases. With the emergence of newer chemoinformatic technologies, existing chemical databases require constant updates to facilitate information accessibility and integration by users. Besides increasing the NPs compound content, the updated SANCDB allows users to access the individual compounds (if available) or their analogs from commercial databases seamlessly.

S, Kumar S. M, Bankapur A, Sinha RK, Simon L, Chidangil S. Effect of OH substitution in 3-benzylchroman-4-ones: crystallographic, CSD, DFT, FTIR, Hirshfeld surface, and energy framework analysis

3-Benzylchroman-4-ones (homoisoflavanones) are oxygen-containing heterocycles with a sixteen-carbon skeleton. They belong to the class of naturally occurring polyphenolic flavonoids with limited occurrence in nature and possess anti-inflammatory, antibacterial, antihistaminic, antimutagenic, antiviral, and angioprotective properties. Recently, we reported the synthesis and anticancer activity studies of fifteen 3-benzylchroman-4-one molecules, and most of them were proven to be effective against BT549 and HeLa cells. In this work, we report the single-crystal X-ray crystallographic studies of two molecules 3-[(2-hydroxyphenyl)methyl]-3,4-dihydro-2H-1-benzopyran-4-one and 3-[(2,4-dimethoxyphenyl)methyl]-3,4-dihydro-2H-1-benzopyran-4-one. The single crystals were grown using a novel laser-induced crystallization technique. We observed that the 3-benzylchroman-4-one derivative bearing OH substitution at the 2′ position adopted different conformation due to formation of dimers through O–H⋯O, and C–H⋯O intermolecular hydrogen bondings. The role of OH substitution in the aforementioned conformational changes was evaluated using density functional theory (DFT), Hirshfeld surface, energy framework and FTIR spectroscopy analysis. In addition, we have carried out a Cambridge Structural Database (CSD) study to understand the conformational changes using five analogue structures. X-ray crystallographic, computational, and spectroscopic studies of 3-benzylchroman-4-ones provided an insight into the role of substitution at benzyl moieties in stabilizing the three-dimensional (3D) structures.

Laser-induced crystallization, single crystal X-ray crystallography, CSD, DFT, FTIR, Hirshfeld surface, and energy frameworks analysis of two new 3-benzylchroman-4-one structures.

Characterization of PMI-5011 on the Regulation of Deubiquitinating Enzyme Activity in Multiple Myeloma Cell Extracts

Deubiquitinating enzyme (DUB)-targeted therapeutics have shown promise in recent years as alternative cancer therapeutics, especially when coupled with proteasome-based inhibitors. While a majority of DUB-based therapeutics function by inhibiting DUB enzymes, studies show that positive regulation of these enzymes can stabilize levels of protein degradation. Unfortunately, there are currently no clinically available therapeutics for this purpose. The goal of this work was to understand the effect of a botanical extract from Artemisia dracunculus L called PMI-5011 on DUB activity in cancer cells. Through a series of kinetic analyses and mathematical modeling, it was found that PMI-5011 positively regulated DUB activity in two model multiple myeloma cells line (OPM2 and MM.1S). This suggests that PMI-5011 interacts with the active domains of DUBs to enhance their activity directly or indirectly, without apparently affecting cellular viability. Similar kinetic profiles of DUB activity were observed with three bioactive compounds in PMI-5011 (DMC-1, DMC-2, davidigenin). Interestingly, a differential cell line-independent trend was observed at higher concentrations which suggested variances in inherent gene expressions of UCHL1, UCHL5, USP7, USP15, USP14, and Rpn11 in OPM2 and MM.1S cell lines. These findings highlight the therapeutic potential of PMI-5011 and its selected bioactive compounds in cancer.

Conformational flexibility in amidophosphoesters: a CSD analysis completed with two new crystal structures of (C6H5O)2P(O)X [X = NHC7H13 and N(CH2C6H5)2]

The crystal structures of diphenyl (cycloheptylamido)phosphate, C19H24NO3P or (C6H5O)2P(O)(NHC7H13), (I), and diphenyl (dibenzylamido)phosphate, C26H24NO3P or (C6H5O)2P(O)[N(CH2C6H5)2], (II), are reported. The NHC7H13 group in (I) provides two significant hydrogen-donor sites in N—H...O and C—H...O hydrogen bonds, needed for a one-dimensional hydrogen-bond pattern along [100] in the crystal, while (II), with a (C6H5CH2)2N moiety, lacks these hydrogen bonds, but its three-dimensional supramolecular structure is mediated by C—H...π interactions. The conformational behaviour of the phenyl rings in (I), (II) and analogous structures from the Cambridge Structural Database (CSD) were studied in terms of flexibility, volume of the other group attached to phosphorus and packing forces. From this study, synclinal (±sc), anticlinal (±ac) and antiperiplanar (±ap) conformations were found to occur. In the structure of (II), there is an intramolecular C ortho —H...O interaction that imposes a +sc conformation for the phenyl ring involved. For the structures from the CSD, the +sc and ±ap conformations appear to be mainly imposed by similar C ortho —H...O intramolecular interactions. The large contribution of the C...H/H...C contacts (32.3%) in the two-dimensional fingerprint plots of (II) is a result of the C—H...π interactions. The differential scanning calorimetry (DSC) analyses exhibit peak temperatures (T m) at 109 and 81 °C for (I) and (II), respectively, which agree with the strengths of the intermolecular contacts and the melting points.

Design and Construction of Aroyl-Hydrazone Derivatives: Synthesis, Crystal Structure, Molecular Docking and Their Biological Activities

Here, we report the synthesis and characterization of four new aroyl-hydrazone derivatives L₁ -L₄ , and their structural as well as biological activities have been explored. In addition to docking with bovine serum albumin (BSA) and duplex DNA, the experimental results demonstrate the effective binding of L₁ -L₄ with BSA protein and calf thymus DNA (ct-DNA) which is in agreement with the docking results. Further biological activities of L₁ -L₄ have been examined through molecular docking with different proteins which are involved in the propagation of viral or cancer diseases. L₁ shows best binding affinity with influenza A virus polymerase PB2 subunit (2VY7) with binding energy -11.42 kcal/mol and inhibition constant 4.23 nm, whereas L₂ strongly bind with the hepatitis C virus NS5B polymerase (2WCX) with binding energy -10.47 kcal/mol and inhibition constant 21.06 nm. Ligand L₃ binds strongly with TGF-beta receptor 1 (3FAA) and L₄ with cancer-related EphA2 protein kinases (1MQB) with binding energy -10.61 kcal/mol, -10.02 kcal/mol and inhibition constant 16.67 nm and 45.41 nm, respectively. The binding energies of L₁ -L₄ are comparable with binding energies of their proven inhibitors. L₁ , L₃ and L₄ can be considered as both 3FAA and 1MQB dual targeting anticancer agents, while L₁ and L₃ are both 2VY7 and 2WCX dual targeting antiviral agents. On the other side, L₂ and L₄ target only one virus related target (2WCX). Furthermore, the geometry optimizations of L₁ -L₄ were performed via density functional theory (DFT). Moreover, all four ligands (L₁ -L₄ ) were characterized by NMR, FT-IR, ESI-MS, elemental analysis and their molecular structures were validated by single crystal X-ray diffraction studies.

Design, synthesis and biological evaluation of novel neuchromenin analogues as potential antifungal agents

In continuation of our program to discover new potential antifungal agents, thirty-two neuchromenin analogues were synthesized and characterized by the spectroscopic analysis. By using the mycelium growth rate method, the target compounds were evaluated systematically for antifungal activities in vitro against six plant pathogenic fungi, and structure-activity relationships (SAR) were derived. Compounds 6b-c, and 6l showed obvious inhibition activity on each of the fungi at 50 μg/mL. For the corresponding fungi, 7 of the compounds showed average inhibition rates of >80% at 50 μg/mL; especially, compounds 6b, 6d-e, and 6i-l displayed more potent antifungal activity against A. solani than that of thiabendazole (a positive control). Moreover, compound 6c also exhibited good activity against C. lunata with EC₅₀ values of 12.7 μg/mL, and the value was much superior to that of thiabendazole (EC₅₀ = 59.7 μg/mL). SAR analysis showed that the presence of conjugated structure, bearing a C=C bond conjugated to the C=O group, obviously decreased the activity; the type and position of the substituted R₅ significantly influenced the activity. Furthermore, the significantly bioactive compounds 6b-e, 6g, 6i and 6l showed very low toxicities against HL-7702, BEL-7402 and HCT-8 cells. Resistance development assay indicated that compounds 6b-e and 6l failed to induce the two tested strains of fungi to develop resistance. SEM analysis initially revealed that compound 6d may exert its antifungal effect by damaging fungal cell wall.