Molecular modeling study, synthesis and biological evaluation of combretastatin A-4 analogues as anticancer agents and tubulin inhibitors

Design, synthesis and inhibition evaluation of novel chalcone amide α-glucosidase inhibitors

Aim: The purpose of this study is to design and synthesize a series of novel chalcone amide α-glucosidase (AG) inhibitors (L1-L10) based on virtual screening and molecular dynamics (MD) simulation. Materials & methods: Target compounds (L1-L10) were synthesized from 2-hydroxyacetophenone and methyl 4-formylbenzoate. Results: In vitro activity test shows that most compounds have good AG inhibition. Specially, compound L4 (IC50 = 8.28 ± 0.04 μM) had the best inhibitory activity, superior to positive control acarbose (IC50 = 8.36 ± 0.02 μM). Molecular docking results show that the good potency of L4 maybe attributed to strong interactions between chalcone skeleton and active site, and the torsion of carbon nitrogen bond in amide group. Conclusion: Compound L4 maybe regard as a good anti-Type II diabetes candidate to preform further study.

Design, synthesis, and biological evaluation of novel benzimidazole derivatives as anti-cervical cancer agents through PI3K/Akt/mTOR pathway and tubulin inhibition

Phosphatidylinositol 3-kinase (PI3K) is one of the most attractive therapeutic targets for cervical cancer treatment. In this study, we designed and synthesized a series of benzimidazole derivatives and evaluated their anti-cervical cancer activity. Compound 4r exhibited strong antiproliferative activity in different cervical cancer cell lines HeLa, SiHa and Ca Ski, and relative lower cytotoxicity to normal hepatic and renal cell lines LO2 and HEK-293t (IC50 values were at 21.08 μM and 23.96 μM respectively). Its IC50 value was at 3.38 μM to the SiHa cells. Further mechanistic studies revealed that 4r induced apoptosis, arrested cell cycle in G2/M phase, suppressed PI3K/Akt/mTOR pathway and inhibit the polymerization of tubulin. Molecular docking study suggested that 4r formed key H-bonds action with PI3Kα (PDB ID:8EXU) and tubulin (PDB ID:1SA0). Zebrafish acute toxicity experiments showed that high concentrations of 4r did not cause death or malformation of zebrafish embryos. All these results demonstrated that 4r would be a promising lead candidate for further development of novel PI3K and tubulin dual inhibitors in cervical cancer treatment.

3,4-Diarylisoxazoles-Analogues of Combretastatin A-4: Design, Synthesis, and Biological Evaluation In Vitro and In Vivo

Focusing on the molecular docking results, a series of 3,4-diarylisoxazoles, analogues of Combretastatin A4, bearing various substituents at the fifth position of the isoxazole ring and pharmacophore groups bioisosteric to methoxy substituent at ring B, were synthesized in good yields and high regioselectivity. Depending on the substituent at C5, three approaches were chosen for the construction of isoxazole ring, including nitrosation of gem-dihalocyclopropanes, nitrile oxide synthesis, and difluoromethoxylation of isoxazolone to afford 5-haloisoxazoles, 5-unsubstituted isoxazoles, and 5-difluoromethoxyisoxazoles, respectively. Isoxazoles 43 and 45 showed selective cytotoxicity and antitubulin inhibition properties in vitro, with pharmacodynamic profiles closely related to that of CA-4. Both of them slow down tumor growth (66-74%) in mouse xenografts and slightly exceed in effectiveness Combretastatin A4-phosphate itself.

Synthesis and Biological Studies of Benzo[b]furan Derivatives: A Review from 2011 to 2022

The importance of the benzo[b]furan motif becomes evident in the remarkable results of numerous biological investigations, establishing its potential as a robust therapeutic option. This review presents an overview of the synthesis of and exhaustive biological studies conducted on benzo[b]furan derivatives from 2011 to 2022, accentuating their exceptional promise as anticancer, antibacterial, and antifungal agents. Initially, the discussion focuses on chemical synthesis, molecular docking simulations, and both in vitro and in vivo studies. Additionally, we provide an analysis of the intricate interplay between structure and activity, thereby facilitating comparisons and profoundly emphasizing the applications of the benzo[b]furan motif within the realms of drug discovery and medicinal chemistry.

Computational Approaches to the Rational Design of Tubulin-Targeting Agents

Microtubules are highly dynamic polymers of α,β-tubulin dimers which play an essential role in numerous cellular processes such as cell proliferation and intracellular transport, making them an attractive target for cancer and neurodegeneration research. To date, a large number of known tubulin binders were derived from natural products, while only one was developed by rational structure-based drug design. Several of these tubulin binders show promising in vitro profiles while presenting unacceptable off-target effects when tested in patients. Therefore, there is a continuing demand for the discovery of safer and more efficient tubulin-targeting agents. Since tubulin structural data is readily available, the employment of computer-aided design techniques can be a key element to focus on the relevant chemical space and guide the design process. Due to the high diversity and quantity of structural data available, we compiled here a guide to the accessible tubulin-ligand structures. Furthermore, we review different ligand and structure-based methods recently used for the successful selection and design of new tubulin-targeting agents.

Discovery of dual tubulin-NEDDylation inhibitors with antiproliferative activity

Although various dual-target tubulin inhibitors have been designed and synthesised, no dual tubulin-NEDDylation inhibitors as antiproliferative agents were reported so far. In this work, a series of trimethoxyphenyl analogues as potential dual tubulin-NEDDylation inhibitors were synthesised and evaluated for their antiproliferative activity. Among them, compound C11 exhibited the most potent inhibitory activity with IC₅₀ values of 1.17, 2.48, and 1.47 μM against HepG2, PC3, and MCF7 cells, respectively. In addition, it displayed the potent inhibitory activity against tubulin with an IC₅₀ value of 2.40 μM and obviously inhibited tubulin polymerisation in HepG2 cells. Furthermore, C11 inhibited NEDDylation by a ATP-dependent manner. Molecular docking studies revealed that the methoxy group and dithiocarbamate group of C11 could form hydrogen bonds with residues of tubulin and E1 NEDD8-activating enzyme (NAE). These results suggested that compound C11 was a dual tubulin-NEDDylation inhibitor with antiproliferative activity.

Computer especially AI-assisted drug virtual screening and design in traditional Chinese medicine

BACKGROUND

Traditional Chinese medicine (TCM), as a significant part of the global pharmaceutical science, the abundant molecular compounds it contains is a valuable potential source of designing and screening new drugs. However, due to the un-estimated quantity of the natural molecular compounds and diversity of the related problems drug discovery such as precise screening of molecular compounds or the evaluation of efficacy, physicochemical properties and pharmacokinetics, it is arduous for researchers to design or screen applicable compounds through old methods. With the rapid development of computer technology recently, especially artificial intelligence (AI), its innovation in the field of virtual screening contributes to an increasing efficiency and accuracy in the process of discovering new drugs.

PURPOSE

This study systematically reviewed the application of computational approaches and artificial intelligence in drug virtual filtering and devising of TCM and presented the potential perspective of computer-aided TCM development.

STUDY DESIGN

We made a systematic review following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Then screening the most typical articles for our research.

METHODS

The systematic review was performed by following the PRISMA guidelines. The databases PubMed, EMBASE, Web of Science, CNKI were used to search for publications that focused on computer-aided drug virtual screening and design in TCM.

RESULT

Totally, 42 corresponding articles were included in literature reviewing. Aforementioned studies were of great significance to the treatment and cost control of many challenging diseases such as COVID-19, diabetes, Alzheimer's Disease (AD), etc. Computational approaches and AI were widely used in virtual screening in the process of TCM advancing, which include structure-based virtual screening (SBVS) and ligand-based virtual screening (LBVS). Besides, computational technologies were also extensively applied in absorption, distribution, metabolism, excretion and toxicity (ADMET) prediction of candidate drugs and new drug design in crucial course of drug discovery.

CONCLUSIONS

The applications of computer and AI play an important role in the drug virtual screening and design in the field of TCM, with huge application prospects.

Discovery of 4-methoxy-N-(1-naphthyl)benzenesulfonamide derivatives as small molecule dual-target inhibitors of tubulin and signal transducer and activator of transcription 3 (STAT3) based on ABT-751

Overexpressed tubulin and continuously activated STAT3 play important roles in the development of many cancers and are potential therapeutic targets. A series of 4-methoxy-N -(1-naphthalene) benzenesulfonamide derivatives were designed and optimized based on β-tubulin inhibitor ABT-751 to verify whether STAT3 and tubulin dual target inhibitors have better antitumor effects. Compound DL14 showed strong inhibitory activity against A549, MDA-MB-231 and HCT-116 cells in vitro with IC50 values of 1.35 μM, 2.85 μM and 3.04 μM, respectively. Further experiments showed that DL14 not only competitively bound to colchicine binding site to inhibit tubulin polymerization with IC50 values 0.83 μM, but also directly bound to STAT3 protein to inhibit STAT3 phosphorylation with IC50 value of 6.84 μM. Three other compounds (TG03, DL15, and DL16) also inhibit this phosphorylation. In terms of single target inhibition, DL14 is slightly inferior to positive drugs, but it shows a good anti-tumor effect in vivo, and can inhibit >80% of xenograft tumor growth. This study describes a novel 4-methoxy-N-(1-naphthyl) benzenesulfonamide skeleton as an effective double-targeted anticancer agent targeting STAT3 and tubulin.

Design, synthesis and biological evaluation of oxalamide derivatives as potent neuraminidase inhibitors

A series of novel oxalamide neuraminidase inhibitors were designed and synthesized according to structure-based virtual screening.

Recent Trends in Tubulin-Binding Combretastatin A-4 Analogs for Anticancer Drug Development

Although significant progress over several decades has been evidenced in cancer therapy, there still remains a need for the development of novel and effective therapeutic strategies to treat several relapsed and intractable cancers. In this regard, tubulin protein has become one of the efficient and major targets for anticancer drug discovery. Considering the antimitotic ability, several tubulin inhibitors have been developed to act against various cancers. Among various tubulin inhibitors available, combretastatin-A4 (CA-4), a naturally occurring lead molecule, offers exceptional cytotoxicity (including the drug-resistant cell lines) and antivascular effects. Although CA-4 offers exceptional therapeutic efficacy, several new advancements have been proposed, such as the structural modification via A and B rings, as well as cis-olefinic bridging, which provide highly efficient analogs with improved tubulin-binding efficiency to meet the anticancer drug development requirements. This review systematically emphasizes the recent trends and latest developments in the anticancer drug design & discovery, using CA-4 analogs as the tubulin inhibiting agents, highlighting their structure-activity relationships (SAR) and resultant pharmacological efficacies.

Molecular interaction of cytotoxic anticancer analogues as inhibitors of β-tubulin protein against UACC-62 melanoma cell

In previous research, a series of cytotoxic anticancer analogues related to 2-acylamino-1,4-naphthoquinone derivatives has been demonstrated. As microtubule plays an important role in many essential cellular processes such as mitosis, tubulin is an important target of anticancer drug. This study performed molecular docking simulation, pharmacophore model, comparative force field analysis model and comparative similarity indices analysis model to investigate the relationship between inhibitory activities and the properties of compounds, in order to further progress the development of cytotoxic anticancer analogues. These compounds have common H-bond interactions with key residues Lys254 and Lys352, but compounds with large R2 substituent have different docking poses than compounds with small R2 substituent. Some of derivatives such as compound 18 formed the H-bonds with residue Lys254 using the oxygen atoms in R1 substituent and formed π-cation interactions with residue Lys352 using phenyl moiety of 1,4-naphthoquinone. The R1 substituent of these compounds preferred to have disfavoured hydrophobic fields and favourable space towards the direction of residue Asn258, while the R2 substituent of these compounds preferred to have about 2-3 carbon chain length hydrophobic substituent towards the direction of residues Ala316 and Lys352. These results offer some beneficial advices for further study in anticancer drug development process.

Design and discovery of new antiproliferative 1,2,4-triazin-3(2H)-ones as tubulin polymerization inhibitors targeting colchicine binding site

Thirty-five new colchicine binding site inhibitors have been designed and synthesized based on the 1,2,4-triazin-3(2H)-one nucleus. Such molecules were synthesized through a cascade reaction between readily accessible α-amino ketones and phenyl carbazate as a masked N-isocyanate precursor. The synthesized derivatives are cisoid restricted combretastatin A4 analogues containing 1,2,4-triazin-3(2H)-one in place of the olefinic bond, and they have the same essential pharmacophoric features of colchicine binding site inhibitors. The synthesized compounds were evaluated in vitro for their antiproliferative activities against a panel of three human cancer cell lines (MCF-7, HepG-2, and HCT-116), using colchicine as a positive control. Among them, two compounds 5i and 6i demonstrated a significant antiproliferative effect against all cell lines with IC₅₀ ranging from 8.2 - 18.2 µM. Further investigation was carried out for the most active cytotoxic agents as tubulin polymerization inhibitors. Compounds 5i and 6i effectively inhibited microtubule assembly with IC₅₀ values ranging from 3.9 to 7.8 µM. Tubulin polymerization assay results were found to be comparable with the cytotoxicity results. The cell cycle analysis revealed significant G2/M cell cycle arrest of the analogue 5i in HepG-2 cells. The most active compounds 4i, 4j, 5 g, 5i and 6i did not induce significant cell death in normal human lung cells Wl-38, suggesting their selectivity against cancer cells. Also, These compounds upregulated the level of active caspase-3 and boosted the levels of the pro-apoptotic protein Bax by five to seven folds in comparison to the control. Moreover, apoptosis analyses were conducted for compound 5i to evaluate its apoptotic potential. Finally, in silico studies were conducted to reveal the probable interaction with the colchicine binding site. ADME prediction study of the designed compounds showed that they are not only with promising tubulin polymerization inhibitory activity but also with favorable pharmacokinetic and drug-likeness properties.

Structural Investigations of Aroylindole Derivatives through 3D-QSAR and Multiple Pharmacophore Modeling for the Search of Novel Colchicines Inhibitor

Background :

The ligand and structure based integrated strategies are being repeatedly and effectively employed for the precise search and design of novel ligands against various disease targets. Aroylindole derivative has a similar structural analogy as Combretastatin A-4, and exhibited potent anticancer activity on several cancer cell lines.

Objective:

To identify structural features of aroylindole derivatives through 3D-QSAR and multiple pharmacophore modelling for the search of novel colchicines inhibitor via virtual screening.

Method:

The present study utilizes ligand and structure based methodology for the establishment of structure activity correlation among trimethoxyaroylindole derivatives and the search of novel colchicines inhibitor via virtual screening. The 3D-QSAR studies were performed using Phase module and provided details of relationship between structure and biological activity. A single ligand based pharmacophore model was generated from Phase on compound 3 and compound 29 and three energetically optimized structure based pharmacophore models were generated from epharmacophore for co-crystallized ligand, compound 3 and compound 29 with protein PBD ID 1SA0, 5EYP and 5LYJ. These pharmacophoric features containing hit-like compounds were collected from commercially available ZINC database and screened using virtual screening workflow.

Results and Discussion:

The 3D-QSAR model studies with good PLSs statistics for factor four was characterized by the best prediction coefficient Q2 (0.8122), regression R2 (0.9405), SD (0.2581), F (102.7), P (1.56e-015), RMSE (0.402), Stability (0.5411) and Pearson-r (0.9397). The generated epharmacophores have GH scores over 0.5 and AUAC ≥ 0.7 indicated that all the pharmacophores were suitable for pharmacophore-based virtual screening. The virtual screened compounds ZINC12323179, ZINC01642724, and ZINC14238006 have showed similar structural alignment as co-crystallized ligand and showed the hydrogen bonding of ligand with ASN101, SER178, THR179, VAL238, CYS241 amino acid of protein.

Conclusion:

The study illustrates that the ligand and structure based pharmacophoric approach is beneficial for identification of structurally diverse hits, having better binding affinity on colchicines binding site as novel anticancer agents.