Pharmacophore-Based Hypothesis Combined with Molecular Docking Protocol for the Screening of Anticancer Compounds from Streptomyces sp.

The POTE family comprises 14 paralogues and is primarily expressed in Prostrate, Placenta, Ovary, Testis, Embryo (POTE), and cancerous cells. The prospective function of the POTE protein family under physiological conditions is less understood. We systematically analyzed their cellular localization and molecular docking analysis to elucidate POTE proteins' structure, function, and Adaptive Divergence. Our result discerns that group three POTE paralogs (POTEE, POTEF, POTEI, POTEJ, and POTEKP (a pseudogene)) exhibits significant variation among other members could be because of their Adaptive Divergence. Furthermore, our molecular docking studies on POTE protein revealed the highest binding affinity with NCI-approved anticancer compounds. Additionally, POTEE, POTEF, POTEI, and POTEJ were subject to an explicit molecular dynamic simulation for 50ns. MM-GBSA and other essential electrostatics were calculated that showcased that only POTEE and POTEF have absolute binding affinities with minimum energy exploitation. Thus, this study's outcomes are expected to drive cancer research to successful utilization of POTE genes family as a new biomarker, which could pave the way for the discovery of new therapies.

Download Full-text

Molecular docking approach to identify potential anticancer compounds from Begonia (Begonia sp)

10.1063/1.4958513 ◽

2016 ◽

Cited By ~ 2

Author(s):

Muhammad Sulaiman Zubair ◽

Syariful Anam ◽

Akhmad Khumaidi ◽

Yuliet Susanto ◽

Mohammad Hidayat ◽

...

Keyword(s):

Molecular Docking ◽

Anticancer Compounds ◽

Docking Approach

Download Full-text

Design and Synthesis of a New Series of 3,5-Disubstituted-1,2,4-Oxadiazoles as Potential Colchicine Binding Site Inhibitors: Antiproliferative activity, Molecular docking, and SAR Studies

New Journal of Chemistry ◽

10.1039/d1nj02885e ◽

2021 ◽

Author(s):

Rana Tarek Diab ◽

Zakaria Abdelsamii ◽

Eatedal Hassan Abd-Elaal ◽

Ahmed A. Al-Karmalawy ◽

Nader Elmaghwry AboDya

Keyword(s):

Molecular Docking ◽

Binding Site ◽

Antiproliferative Activity ◽

Research Area ◽

Pharmaceutical Companies ◽

Anticancer Compounds ◽

Design And Synthesis ◽

Sar Studies ◽

Colchicine Binding Site ◽

Research Institutes

The development of anticancer compounds targeting the colchicine-binding site of tubulin, termed colchicine-binding site inhibitors (CBSIs) is a promising research area for pharmaceutical companies and research institutes. A series of...

Download Full-text

Exploring Different Virtual Screening Strategies for Acetylcholinesterase Inhibitors

BioMed Research International ◽

10.1155/2013/236850 ◽

2013 ◽

Vol 2013 ◽

pp. 1-8 ◽

Cited By ~ 6

Author(s):

Nibha Mishra ◽

Arijit Basu

Keyword(s):

Molecular Docking ◽

Virtual Screening ◽

Similarity Search ◽

Acetylcholinesterase Inhibitors ◽

Enrichment Factors ◽

Pharmacophore Modeling ◽

Receiver Operating Curve ◽

Ache Inhibitors ◽

Docking Protocol ◽

Screening Strategies

The virtual screening problems associated with acetylcholinesterase (AChE) inhibitors were explored using multiple shape, and structure-based modeling strategies. The employed strategies include molecular docking, similarity search, and pharmacophore modeling. A subset from directory of useful decoys (DUD) related to AChE inhibitors was considered, which consists of 105 known inhibitors and 3732 decoys. Statistical quality of the models was evaluated by enrichment factor (EF) metrics and receiver operating curve (ROC) analysis. The results revealed that electrostatic similarity search protocol using EON (ET_combo) outperformed all other protocols with outstanding enrichment of>95% in top 1% and 2% of the dataset with an AUC of 0.958. Satisfactory performance was also observed for shape-based similarity search protocol using ROCS and PHASE. In contrast, the molecular docking protocol performed poorly with enrichment factors<30% in all cases. The shape- and electrostatic-based similarity search protocol emerged as a plausible solution for virtual screening of AChE inhibitors.

Download Full-text

Accurate Prediction of Inhibitor Binding to HIV-1 Protease Using CANDOCK

Frontiers in Chemistry ◽

10.3389/fchem.2021.775513 ◽

2022 ◽

Vol 9 ◽

Author(s):

Zackary Falls ◽

Jonathan Fine ◽

Gaurav Chopra ◽

Ram Samudrala

Keyword(s):

Molecular Docking ◽

Characteristic Curve ◽

Scoring Function ◽

Hiv Protease ◽

Binding Affinities ◽

Knowledge Based ◽

Pearson Coefficient ◽

Docking Protocol ◽

Immunodeficiency Virus ◽

Hiv 1

The human immunodeficiency virus 1 (HIV-1) protease is an important target for treating HIV infection. Our goal was to benchmark a novel molecular docking protocol and determine its effectiveness as a therapeutic repurposing tool by predicting inhibitor potency to this target. To accomplish this, we predicted the relative binding scores of various inhibitors of the protease using CANDOCK, a hierarchical fragment-based docking protocol with a knowledge-based scoring function. We first used a set of 30 HIV-1 protease complexes as an initial benchmark to optimize the parameters for CANDOCK. We then compared the results from CANDOCK to two other popular molecular docking protocols Autodock Vina and Smina. Our results showed that CANDOCK is superior to both of these protocols in terms of correlating predicted binding scores to experimental binding affinities with a Pearson coefficient of 0.62 compared to 0.48 and 0.49 for Vina and Smina, respectively. We further leveraged the Database of Useful Decoys: Enhanced (DUD-E) HIV protease set to ascertain the effectiveness of each protocol in discriminating active versus decoy ligands for proteases. CANDOCK again displayed better efficacy over the other commonly used molecular docking protocols with area under the receiver operating characteristic curve (AUROC) of 0.94 compared to 0.71 and 0.74 for Vina and Smina. These findings support the utility of CANDOCK to help discover novel therapeutics that effectively inhibit HIV-1 and possibly other retroviral proteases.

Download Full-text

In vitro evaluation and molecular docking analysis of potential anticancer compounds from Annona muricata L.

10.21203/rs.3.rs-172301/v1 ◽

2021 ◽

Author(s):

Pichai Nalini ◽

Kalibulla Syed Ibrahim ◽

Durairaj Brindha

Keyword(s):

Molecular Docking ◽

Docking Studies ◽

Mass Spectrometry Data ◽

Annona Muricata ◽

Anticancer Activities ◽

Anticancer Compounds ◽

Cytotoxic Effects ◽

Standard Drug ◽

Cytotoxicity Studies

Abstract Annona muricata L. is widely distributed in tropical and subtropical regions around the world. Traditionally this plant has been used as a medicine for multiple ailments including cancer. The present study focussed on the anticancer activities of hydroethanolic extracts of leaves of A. muricata L. on Dalton’s Lymphoma Ascites (DLA) cell line in comparison with standard drug doxorubicin. Cytotoxicity studies have indicated that the phytoconstituents of A. muricata have the ability to selectively target cancer cells (IC50 = 185.585 µg/ml), whereas minimal or negligible cytotoxic effects were observed on normal cells. Gas Chromatography - Mass Spectrometry data revealed the presence of 16 phytoconstituents comprising mainly alkaloids and phenolic compounds. Pharmacokinetic profiling and molecular docking studies using the phytoconstituents were performed in order to gain a better understanding of the putative mechanisms of action leading to the development of improved and affordable therapies.

Download Full-text

Antimicrobial Activity of a Novel Secondary Metabolite from Streptomyces sp. and Molecular Docking Studies against Bacterial Leaf Blight Pathogen of Rice

International Journal of Current Microbiology and Applied Sciences ◽

10.20546/ijcmas.2017.611.337 ◽

2017 ◽

Vol 6 (11) ◽

pp. 2861-2870

Author(s):

Nanjundan Jaivel ◽

Ramasamy Rajesh ◽

Devadasan Velmurugan ◽

Ponnusamy Marimuthu

Keyword(s):

Antimicrobial Activity ◽

Molecular Docking ◽

Secondary Metabolite ◽

Docking Studies ◽

Leaf Blight ◽

Bacterial Leaf Blight ◽

Streptomyces Sp ◽

Molecular Docking Studies

Download Full-text

In silico study of lutein as anti-HER-2 receptors in breast cancer treatment

Pharmacy Reports ◽

10.51511/pr.17 ◽

2021 ◽

Vol 1 (1) ◽

pp. 17

Author(s):

Ni Ketut Nitya Cahyani ◽

Wahyu Nadi Eka Putri ◽

I Kadek Diva Dwivayana ◽

Ni Putu Dinda Mirayanti ◽

Ni Putu Linda Laksmiani

Keyword(s):

Breast Cancer ◽

Molecular Docking ◽

Binding Energy ◽

Cancer Progression ◽

In Silico ◽

Mechanism Of Inhibition ◽

Docking Protocol ◽

In Silico Study ◽

Her 2 ◽

In Silico Molecular Docking

Human Epidermal Receptor-2 (HER-2) overexpression is implicated in breast cancer progression; thus, HER-2 is widely used as the target of anticancer therapy. Lapatinib is a drug widely used to inhibit the HER-2 receptor and tyrosine kinase; however, it develops drug resistance. Lutein is promising to be developed as breast cancer therapy. This study aims to determine the mechanism of inhibition of HER-2 receptor overexpression by lutein in silico. Molecular docking was carried out by optimizing the lutein and lapatinib, preparing of protein target HER-2 (PDB ID 3PP0), validating of molecular docking protocol, and docking of lutein and lapatinib on HER-2. The study resulted in the binding energy of -12.37 kcal/mol, while the binding energy of the native ligand and lapatinib to HER-2 was -10.43 kcal/mol and -12.25 kcal/mol, respectively. The binding energy showed that lutein has potential as breast anticancer suggested from the stronger affinity to HER2.

Download Full-text