Discovery of novel inhibitors for Nek6 protein through homology model assisted structure based virtual screening and molecular docking approaches

Design and synthesis of pyridopyrimidines targeting NEK6 kinase

We designed a series of pyrido[2,3-d]pyrimidine derivatives based on the structure of the NEK6 kinase inhibitor, compound 21 (2-amino-5-phenyl-5,11-dihydro-3H-indeno[2',1':5,6]pyrido[2,3-d]pyrimidine-4,6-dione), which share the same heterocyclic core. Chemical modifications, aimed at altering the molecular planarity of 21 to enhance water solubility, were guided by receptor-based ligand design and further supported by molecular docking, molecular dynamics simulations, and free energy perturbation calculations. Our results indicate that disrupting the planarity of 21 increases aqueous solubility - nearly doubling it in two cases- while reducing lipophilicity. Among the compounds tested, three showed both improved solubility and NEK6 inhibitory activity exceeding 50 % in single-dose assay.

NIMA-related kinase-6 (NEK6) as an executable target in cancer

Cancer is a disease that develops when cells begin to divide uncontrollably and spreads to other parts of the body. Proliferation and invasion of cancerous cells are generally known to be influenced by cell cycle-related proteins in human malignancies. Therefore, in this review, we have emphasized on the serine/threonine kinase named NEK6. NEK6 is been deliberated to play a critical role in mitosis progression that includes mitotic spindle formation, metaphase to anaphase transition, and centrosome separation. Moreover, it has a mechanistic role in DNA repair and can cause apoptosis when inhibited. Past studies have connected NEK6 protein expression to cancer cell senescence. Besides, there are reports relating NEK6 to a range of malignancies including breast, lung, ovarian, prostate, kidney, liver, and others. Given its significance, this review attempts to describe the structural and functional aspects of NEK6 in various cellular processes, as well as how it is linked to different forms of cancer. Lastly, we have accentuated, on some of the plausible inhibitors that have been explored against NEK6 overexpression.

Exploring novel and potent molecules for disrupting DEPTOR-mTOR interaction through structure-steered screening, extra-exactitude molecular docking, prime binding free energy estimation and voguish molecular dynamics

Dep domain containing mTOR interacting protein (DEPTOR) has critical implications in the development and progression of human malignancies. Increased expression of DEPTOR promotes the growth of tumor cells by inhibiting the mTORC1, which alleviates the negative feedback inhibition by mTORC1 downstream target S6Ks on PI3K/AKT pathway thereby promotes cell survival and prevents apoptosis. This clearly suggests that targetting DEPTOR-mTOR interactions through small molecules may prove as an effective strategy for circumventing distinct cancers. In this study, we employed a top-down approach for finding three novel molecules which may prove effective in disrupting Deptor-mTOR interaction. Following DEPTOR modelling and validation we performed grid-directed structure-based screening by specifying the residues of DEPTOR known to interact with mTOR. A library of 10,000 protein-protein disrupting molecules was screened against the defined region of DEPTOR. From the screened molecules, 30 molecules with highest binding affinity were chosen for molecular docking. Thirty (30) extra-precision molecular docking experiments and 30 molecular mechanics generalized born surface area (MMGBSA) assays were performed. Following this top 10 molecules in terms of binding affinity were selected and the interaction profile of their corresponding docked files was generated. The top three molecules were finally selected after taking all the three parameters including docking score, binding energy value and interaction profile into consideration. For atomistic insights regarding DEPTOR-topmost hit interactions, molecular dynamics was performed for 100 ns. This molecule after further evaluation may prove as promising candidate for anticancer therapy.Communicated by Ramaswamy H. Sarma.

(5E,7E)-4,5,6 Trihydroxy-3-(hydroxymethyl)tetrahydro-2H-pyran-2-ylheptadeca-5,7-dienoate from Euclea crispa (L.) Inhibits Ovarian Cancer Cell Growth by Controlling Apoptotic and Metastatic Signaling Mechanisms

Bioactive compound (5E,7E)-4,5,6 trihydroxy-3-(hydroxymethyl)tetrahydro-2H-pyran-2-ylheptadeca-5,7-dienoate (compound 2) was isolated from Euclea crispa (E. crispa) by the chromatographic methods. Further, the compound was confirmed by spectroscopic techniques such as ultraviolet-visible (UV/Vis) spectrometer, Fourier transform infrared (FTIR) spectrometer, and 1H and 13C nuclear magnetic resonance (NMR). Compound 2 exhibited a significant antioxidant activity with IC50 values. It restrained the auxesis of HO-8910 cells in a shot-dependent mode. CXCR4, HER2, and Akt proteins involved in cell proliferation and metastasis were found to be significantly reduced (p < 0.05). The protein that is responsible for the death of cells (Bcl-2 and Bcl-xL) was reduced (p < 0.05), while the protein expression of p53 and caspase-9 was increased (p < 0.05) in compound 2-treated HO-8910 cells. The results of molecular docking analysis showed the binding affinity with CXCR4 and HER2. Thus, compound 2 can serve as a promising chemotherapeutic agent for the intervention of ovarian cancer. The findings of this study conclude that compound 2 from E. crispa might work as a potential antioxidative and chemotherapeutic agent. The in vivo studies and attempts will pave way for this compound to be an effective drug hereafter.

Identification of Novel SARS-CoV-2 Inhibitors: A Structure-Based Virtual Screening Approach

The recent outbreak of the coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) in the last few months raised global health concern. Previous research described that remdesivir and ritonavir can be used as effective drugs against COVID-19. In this study, we applied the structure-based virtual screening (SBVS) on the high similar remdesivir- and ritonavir-approved drugs, selected from the DrugBank database as well as on a series of ritonavir derivatives, selected from the literature. The aim was to provide new potent SARS-CoV-2 main protease (Mpro) inhibitors with high stability. The analysis was performed using AutoDock VINA implicated in the PyRx 0.8 tool. Based on the ligand binding energy, 20 compounds were selected and then analyzed by AutoDock tools. Among the 20 compounds, 3 compounds were selected as high-potent anti-COVID-19.

Screening and GC-MS profiling of ethanolic extract of Tylophora pauciflora

Medicinal plants are boundless source of raw materials for the pharmaceutical. Identification of natural compounds from medicinal plant is helpful in the discovery of novel therapeutic agents. Tylophora pauciflora is a medicinal plant, which possess many biological activities such as antioxidant activity, anti-inflammatory activity and anti cancer activity. There is no GC-MS analysis reported on this plant. Thus, the present study is aimed to identify the present of phyto-chemical compounds from ethanolic extract of Tylophora pauciflora using GC-MS analysis. Results, the extract possess totally 14 bioactive compounds among that natural compound of n-hexadecanoic acid has highest % peak area and it have the variety of biological activities such as; anti-oxidant, 5-alpha-reductase-inhibitor, anti-fibrinolytic, hemolytic, antimicrobial activity, hypo-cholesterolemic, nematicide, pesticide, anti-androgenic flavor and hemolytic. It is concluded that the ethanolic extract of Tylophora pauciflora have biologically active compounds. In future by isolating and identifying, these compounds can be considered to treat the human disorders.

Screening of Potential Phytocompounds From Euclea crispa (Thunb.) Leaves Targeting Human Epidermal Growth Factor Receptor 2 (HER2) Signaling Pathway

Background:

Overexpression of human epidermal growth factor receptor 2 (HER2) plays an important role in the development and progression in a variety of cancers and it is a novel therapeutic target for breast cancer and ovarian cancer. Euclea crispa (E. crispa) is a South African medicinal plant in the family Ebenaceae used in the management of different human diseases and disorders.

Aims:

The aim of this study was to evaluate the potential inhibitors against HER2 from hexane extract of E. crispa leaves.

Materials and Methods:

Chemical fingerprinting method was used to identify the presence of natural compounds from the extract whereas their inhibitory activities were analyzed by molecular docking analysis against HER2. Absorption, distribution, metabolism, and excretion (ADME) properties also predicted to establish the pharmacokinetics and pharmacodynamics profiles of the selected compounds.

Results:

The molecular docking analysis expressed that phenyl glucuronide, hydrocortisone acetate, and 6-(4,6-dioxo-1,4,5,6-tetrahydropyrimidin-2-yl-amino)hexanoic acid trifluoroacetate possess good inhibitory activities with good glide score of −6.63, −5.41, and −5.40 and glide energy of −35.03, −42.51, and −31.38 kcal/mol, respectively when compared with standard Food and Drug Administration–approved drug and other compounds. All the screened compounds were within the acceptable and permissible limits of ADME properties.

Conclusion:

Thus, from this study it can be concluded that, these screened natural compounds from E. crispa leaves may serve as potential inhibitors for HER2 and they might lead to development of new therapeutic agents against cancer and its associated complications.

Identification and antitumor activity of a novel inhibitor of the NIMA-related kinase NEK6

The NIMA (never in mitosis, gene A)-related kinase-6 (NEK6), which is implicated in cell cycle control and plays significant roles in tumorigenesis, is an attractive target for the development of novel anti-cancer drugs. Here we describe the discovery of a potent ATP site-directed inhibitor of NEK6 identified by virtual screening, adopting both structure- and ligand-based techniques. Using a homology-built model of NEK6 as well as the pharmacophoric features of known NEK6 inhibitors we identified novel binding scaffolds. Twenty-five compounds from the top ranking hits were subjected to in vitro kinase assays. The best compound, i.e. compound 8 ((5Z)-2-hydroxy-4-methyl-6-oxo-5-[(5-phenylfuran-2-yl)methylidene]-5,6-dihydropyridine-3-carbonitrile), was able to inhibit NEK6 with low micromolar IC₅₀ value, also displaying antiproliferative activity against a panel of human cancer cell lines. Our results suggest that the identified inhibitor can be used as lead candidate for the development of novel anti-cancer agents, thus opening the possibility of new therapeutic strategies.

In depth analysis of kinase cross screening data to identify chemical starting points for inhibition of the Nek family of kinases

Potent, selective, and cell active small molecule kinase inhibitors are useful tools to help unravel the complexities of kinase signaling. As the biological functions of individual kinases become better understood, they can become targets of drug discovery efforts. The small molecules used to shed light on function can also then serve as chemical starting points in these drug discovery efforts. The Nek family of kinases has received very little attention, as judged by number of citations in PubMed, yet they appear to play many key roles and have been implicated in disease. Here we present our work to identify high quality chemical starting points that have emerged due to the increased incidence of broad kinome screening. We anticipate that this analysis will allow the community to progress towards the generation of chemical probes and eventually drugs that target members of the Nek family.

In vitro and in silico characterization of angiogenic inhibitors from Sophora interrupta

Sophora interrupta Bedd, (Fabaceae) is used in Indian folk medicine to treat cancer. Angiogenesis is one of the crucial characteristics of cancer metastasis and is regulated by vascular endothelial growth factor (VEGF). In this study, we examined the antiangiogenic properties of the root ethyl acetate extract of Sophora interrupta by various methods. In vitro antioxidant activity (100-600 μg/ml) of S. interrupta ethyl acetate (SEA) extract was evaluated by DPPH and ABTS, anti-inflammatory activity (50, 100 and 150 μg/ml) by estimating nitric oxide (NO) levels, anti-angiogenic activity (200 and 500 μg/ml) was validated by chorio allantoic membrane (CAM) assay and in silico molecular dynamic (MD) simulations analyses (25 ns) were performed to identify the anti-angiogenic compounds extracted from root extract. The antioxidative activity of SEA extract at IC₅₀ (200 ± 0.6 μg/mL) is equal to that of ascorbic acid at IC₅₀ (50 ± 0.6 μg/mL), and the anti-inflammatory activity of SEA extract at IC₅₀ (150 ± 0.2 μg/mL) was inhibited significantly by nitric oxide (NO) production. The SEA extract significantly reduced the sprouting of new blood vessels at ID₅₀ 500 ± 0.13 μg/mL in the CAM assay. Gas chromatography-mass spectrometry analysis of the SEA extract detected 34 secondary metabolites, of which 6a,12a-dihydro-6H-(1,3)dioxolo(5,6)benzofuro(3,2-c)chromen-3-ol (maackiain) and funiculosin formed strong hydrogen bond interactions with Lys 920, Thr 916 and Cys 919 (2H), as well as Glu 917 of VEGFR2, and these interactions were similar to those of the anti-angiogenic compound axitinib. Significant findings in all the assays performed indicate that SEA extract has potential anti-angiogenic compounds that may interfere with VEGF-induced cancer malignancy.

Binding Free Energy Calculations of Nine FDA-approved Protease Inhibitors Against HIV-1 Subtype C I36T↑T Containing 100 Amino Acids Per Monomer

In this work, have investigated the binding affinities of nine FDA-approved protease inhibitor drugs against a new HIV-1 subtype C mutated protease, I36T↑T. Without an X-ray crystal structure, homology modelling was used to generate a three-dimensional model of the protease. This and the inhibitor models were employed to generate the inhibitor/I36T↑T complexes, with the relative positions of the inhibitors being superimposed and aligned using the X-ray crystal structures of the inhibitors/HIV-1 subtype B complexes as a reference. Molecular dynamics simulations were carried out on the complexes to calculate the average binding free energies for each inhibitor using the molecular mechanics generalized Born surface area (MM-GBSA) method. When compared to the binding free energies of the HIV-1 subtype B and subtype C proteases (calculated previously by our group using the same method), it was clear that the I36T↑T proteases mutations and insertion had a significant negative effect on the binding energies of the non-pepditic inhibitors nelfinavir, darunavir and tipranavir. On the other hand, ritonavir, amprenavir and indinavir show improved calculated binding energies in comparison with the corresponding data for wild-type C-SA protease. The computational model used in this study can be used to investigate new mutations of the HIV protease and help in establishing effective HIV drug regimes and may also aid in future protease drug design.

Kinase inhibitor profile for human nek1, nek6, and nek7 and analysis of the structural basis for inhibitor specificity

Human Neks are a conserved protein kinase family related to cell cycle progression and cell division and are considered potential drug targets for the treatment of cancer and other pathologies. We screened the activation loop mutant kinases hNek1 and hNek2, wild-type hNek7, and five hNek6 variants in different activation/phosphorylation statesand compared them against 85 compounds using thermal shift denaturation. We identified three compounds with significant Tm shifts: JNK Inhibitor II for hNek1(Δ262-1258)-(T162A), Isogranulatimide for hNek6(S206A), andGSK-3 Inhibitor XIII for hNek7wt. Each one of these compounds was also validated by reducing the kinases activity by at least 25%. The binding sites for these compounds were identified by in silico docking at the ATP-binding site of the respective hNeks. Potential inhibitors were first screened by thermal shift assays, had their efficiency tested by a kinase assay, and were finally analyzed by molecular docking. Our findings corroborate the idea of ATP-competitive inhibition for hNek1 and hNek6 and suggest a novel non-competitive inhibition for hNek7 in regard to GSK-3 Inhibitor XIII. Our results demonstrate that our approach is useful for finding promising general and specific hNekscandidate inhibitors, which may also function as scaffolds to design more potent and selective inhibitors.