From Natural Compounds to Bioactive Molecules through NMR and In Silico Methodologies

2020 ◽  
Author(s):  
Simona De Vita ◽  
Stefania Terracciano ◽  
Ines Bruno ◽  
Maria Giovanna Chini
Keyword(s):  
In Silico ◽  
Natural Compounds ◽  
Bioactive Molecules

Novel Spiro/non-Spiro Pyranopyrazoles: Eco-Friendly Synthesis, In-vitro Anticancer Activity, DNA Binding, and In-silico Docking Studies

2019 ◽  
Vol 15 (2) ◽  
pp. 257-267 ◽  
Author(s):  
Paritosh Shukla ◽  
Ashok Sharma ◽  
Leena Fageria ◽  
Rajdeep Chowdhury
Keyword(s):  
Anticancer Activity ◽  
Anticancer Agents ◽  
In Silico ◽  
Antimicrobial Agents ◽  
Docking Studies ◽  
Bioactive Molecules ◽  
Microwave Assisted Synthesis ◽  
Binding Affinities ◽  
In Silico Docking

Background: Cancer being a deadly disease, many reports of new chemical entities are available. Pyranopyrazole (PPZ) compounds have also been disclosed as bioactive molecules but mainly as antimicrobial agents. Based on one previous report and our interest in anticancer drug design, we decided to explore PPZs as anticancer agents. To the best of our knowledge, we found that a comprehensive study, involving synthesis, in-vitro biological activity determination, exploration of the mechanism of inhibition and finally in-silico docking studies, was missing in earlier reports. This is what the present study intends to accomplish. Methods: Ten spiro and eleven non-spiro PPZ molecules were synthesized by environment-friendly multicomponent reaction (MCR) strategy. After subjecting each of the newly synthesized molecules to Hep3b hepatocellular carcinoma cell lines assay, we selectively measured the Optical Density (OD) of the most active ones. Then, the compound exhibiting the best activity was docked against human CHK- 1 protein to get an insight into the binding affinities and a quick structure activity relationship (SAR) of the PPZs. Results: The two series of spiro and non-spiro PPZs were easily synthesized in high yields using microwave assisted synthesis and other methods. Among the synthesized compounds, most compounds showed moderate to good anticancer activity against the MTT assay. After performing the absorbance studies we found that the non-spiro molecules showed better apoptosis results and appeared to bind to DNA causing disruption in their structures. Finally, the docking results of compound 5h (having N,Ndimethylamino substituted moiety) clearly showed good binding affinities as predicted by our experimental findings. Conclusion: The paper describes a comprehensive synthesis, in-vitro and docking studies done on new PPZs. The newly synthesized series of spiro and non-spiro PPZs were found to possess antineoplasmic activity as evinced by the studies on hep3b cells. Also, the UV visible absorbance study gave clues to the possible binding of these molecules to the DNA. Docking studies corroborated well with the experimental results. Thus, these new molecules appear to be potential anticancer agents, but further studies are required to substantiate and elaborate on these findings.

Natural Compounds and Drug Discovery: Can Cnidarian Venom Play a Role?

2019 ◽  
Vol 19 (2) ◽  
pp. 114-118
Author(s):  
Gian Luigi Mariottini ◽  
Irwin Darren Grice
Keyword(s):  
Biological Activity ◽  
Marine Species ◽  
Natural Compounds ◽  
Therapeutic Agents ◽  
Industrial Applications ◽  
Bioactive Molecules ◽  
Sea Anemones ◽  
Therapeutic Approaches ◽  
Ongoing Research ◽  
Biological Compounds

Natural compounds extracted from organisms and microorganisms are an important resource for the development of drugs and bioactive molecules. Many such compounds have made valuable contributions in diverse fields such as human health, pharmaceutics and industrial applications. Presently, however, research on investigating natural compounds from marine organisms is scarce. This is somewhat surprising considering that the marine environment makes a major contribution to Earth's ecosystems and consequently possesses a vast storehouse of diverse marine species. Interestingly, of the marine bioactive natural compounds identified to date, many are venoms, coming from Cnidarians (jellyfish, sea anemones, corals). Cnidarians are therefore particularly interesting marine species, producing important biological compounds that warrant further investigation for their development as possible therapeutic agents. From an experimental aspect, this review aims to emphasize and update the current scientific knowledge reported on selected biological activity (antiinflammatory, antimicrobial, antitumoral, anticoagulant, along with several less studied effects) of Cnidarian venoms/extracts, highlighting potential aspects for ongoing research towards their utilization in human therapeutic approaches.

scholarly journals Plant-Derived Anticancer Compounds as New Perspectives in Drug Discovery and Alternative Therapy

Molecules ◽  
2021 ◽  
Vol 26 (4) ◽  
pp. 1109
Author(s):  
Cristina Adriana Dehelean ◽  
Iasmina Marcovici ◽  
Codruta Soica ◽  
Marius Mioc ◽  
Dorina Coricovac ◽  
...  
Keyword(s):  
Targeted Delivery ◽  
Alternative Therapy ◽  
Natural Compounds ◽  
Mechanisms Of Action ◽  
Chemotherapeutic Agents ◽  
Biologically Active ◽  
Bioactive Molecules ◽  
Multi Drug Resistance ◽  
Chemopreventive Agents ◽  
Pharmaceutical Agents

Despite the recent advances in the field of chemically synthetized pharmaceutical agents, nature remains the main supplier of bioactive molecules. The research of natural products is a valuable approach for the discovery and development of novel biologically active compounds possessing unique structures and mechanisms of action. Although their use belongs to the traditional treatment regimes, plant-derived compounds still cover a large portion of the current-day pharmaceutical agents. Their medical importance is well recognized in the field of oncology, especially as an alternative to the limitations of conventional chemotherapy (severe side effects and inefficacy due to the occurrence of multi-drug resistance). This review offers a comprehensive perspective of the first blockbuster chemotherapeutic agents of natural origin’s (e.g. taxol, vincristine, doxorubicin) mechanism of action using 3D representation. In addition is portrayed the step-by-step evolution from preclinical to clinical evaluation of the most recently studied natural compounds with potent antitumor activity (e.g. resveratrol, curcumin, betulinic acid, etc.) in terms of anticancer mechanisms of action and the possible indications as chemotherapeutic or chemopreventive agents and sensitizers. Finally, this review describes several efficient platforms for the encapsulation and targeted delivery of natural compounds in cancer treatment

scholarly journals High Throughput in Silico Identification of Novel Phytochemical Inhibitors for the Master Regulator of Inflammation (TNFα)

2021 ◽  
Author(s):  
Pratap Kumar Parida ◽  
Dipak Paul ◽  
Debamitra Chakravorty
Keyword(s):  
Small Molecule ◽  
High Throughput ◽  
In Silico ◽  
Small Molecule Inhibitors ◽  
Binding Free Energy ◽  
Natural Compounds ◽  
Free Energy Calculations ◽  
Compound Libraries ◽  
Relative Binding

<p><a>The over expression of Tumor necrosis factor-α (TNFα) has been implicated in a variety of disease and is classified as a therapeutic target for inflammatory diseases (Crohn disease, psoriasis, psoriatic arthritis, rheumatoid arthritis).Commercially available therapeutics are biologics which are associated with several risks and limitations. Small molecule inhibitors and natural compounds (saponins) were identified by researchers as lead molecules against TNFα, however, </a>they were often associated with high IC50 values which can lead to their failure in clinical trials. This warrants research related to identification of better small molecule inhibitors by screening of large compound libraries. Recent developments have demonstrated power of natural compounds as safe therapeutics, hence, in this work, we have identified TNFα phytochemical inhibitors using high throughput <i>in silico </i>screening approaches of 6000 phytochemicals followed by 200 ns molecular dynamics simulations and relative binding free energy calculations. The work yielded potent hits that bind to TNFα at its dimer interface. The mechanism targeted was inhibition of oligomerization of TNFα upon phytochemical binding to restrict its interaction with TNF-R1 receptor. MD simulation analysis resulted in identification of two phytochemicals that showed stable protein-ligand conformations over time. The two compounds were triterpenoids: Momordicilin and Nimbolin A with relative binding energy- calculated by MM/PBSA to be -190.5 kJ/Mol and -188.03 kJ/Mol respectively. Therefore, through this work it is being suggested that these phytochemicals can be used for further <i>in vitro</i> analysis to confirm their inhibitory action against TNFα or can be used as scaffolds to arrive at better drug candidates.</p>

In silico drug design: development of new pyrimidine-based benzo-thiazole derivatives, selective for CDK2

2021 ◽  
Vol 18 ◽  
Author(s):  
Rania Kasmi ◽  
Larbi Elmchichi ◽  
Abdellah El Aissouq ◽  
Mohammed Bouachrine ◽  
Abdelkrim Ouammou
Keyword(s):  
Colon Cancer ◽  
Molecular Docking ◽  
In Silico ◽  
3D Qsar ◽  
Bioactive Molecules ◽  
Cancer Drugs ◽  
Qsar Studies ◽  
Benzothiazole Derivatives ◽  
Docking Approach ◽  
Potential Inhibitors

Backgroud: Kinases are proteins that control many biological functions. They are involved in cellular regulation, and many of them are deregulated in cancer proliferation. The evidence of this deregulation in many pathologies served as the origin of kinases as a therapeutic class and constitutes the motive that leads numerous teams to search for inhibitors of these targets. Objective: Based on 3D-QSAR studies and the molecular docking approach, we have developed new potential inhibitors that could be optimized and transformed into colon cancer drugs. Objective: Based on 3D-QSAR studies and the molecular docking approach, we have developed new potential inhibitors that could be optimized and transformed into colon cancer drugs. Method: To design new bioactive molecules and study their interactions with the cyclin-depend kinase type 2 (CDK2) enzyme, we used two virtual screening methods: 3D-QSAR modeling and molecular docking on a series of 28 pyrimidine-based benzothiazole derivatives. Results: To develop models (3D QSAR) we used CoMFA and CoMSIA techniques using SYBYL-X2.0 molecular modeling software. The statistical parameters reveal that the good CoMFA model displays (Q²= 0.587; R²= 0.895) and that of CoMSIA displays (Q²= 0.552; R²= 0.768) which are considered to be very good internal prediction values, while an external validation of a test series of 5 compounds not included in the model development series gives R²test values of 0.56 for CoMFA and R²test values of 0.51 for CoMSIA. The molecular docking approach with AutoDockTools-1.5.6 is introduced in this work to enrich the interpretations extracted from the CoMFA and CoMSIA contour maps, and to provide an in silico research method for the most favorable mode of interaction of an inhibitor within its receptor (CDK2). Conclusion: We have constructed and validated a quantitative 3D model of structure-activity relation-ships of pyrimidine-based benzothiazole derivatives as CDK2 inhibitors. This model allows us to identify the nature and position of the groups that enhance the activity, giving us directions to discover new, more powerful molecules in a limited time.

scholarly journals Bioactive molecules modelised by numerical simulation:molecules against Escherichia Coli

2014 ◽  
Vol 70 (a1) ◽  
pp. C1008-C1008
Author(s):  
Rita Kakou Yao ◽  
Jules Abodou Tenon ◽  
Akoun Abou
Keyword(s):  
Escherichia Coli ◽  
Biological Activity ◽  
In Silico ◽  
Biological Activities ◽  
Digital Simulation ◽  
Simulation Method ◽  
Bioactive Molecules ◽  
Structural Determination ◽  
Human Beings

The work exposed in this paper joins in the research of medecine by means of the modelling by digital simulation (method in silico). This method allows to plan the biological activities of new molecules and to design others more active than existing molecules against a given infection . The generated and validated models are used here in the research for molecules potentially more active against Escherichia coli which causes diarrheic infections at the human beings. Here, we report works the synthesis of our works of structural determination, of forecast of biological activity and conception of molecules bioactive again Eschericha coli.

scholarly journals INHIBITION OF α-AMYLASE AND α-GLUCOSIDASE BY (6RS)-22-HYDROXY-23,24,25,26,27-PENTANOR-VITAMIN-D3-6,19-SULFUR DIOXIDE-ADDUCT, MANOALIDE AND 5β-CHOLESTANE-3α,7α,12α,24,25,26-HEXOL ISOLATED FROM ACETONE EXTRACT OF HELIANTHUS ANNUUS L. SEEDS

2018 ◽  
Vol 10 (5) ◽  
pp. 39 ◽  
Author(s):  
Varsha V. Sonkamble ◽  
Nilesh S. Wagh ◽  
Laxmikant H. Kamble
Keyword(s):  
Helianthus Annuus ◽  
Vitamin D3 ◽  
In Silico ◽  
Binding Energies ◽  
Acetone Extract ◽  
Bioactive Molecules ◽  
Total Phenolic ◽  
Helianthus Annuus L ◽  
Kinetics Studies

Objective: This investigation includes characterization of phytochemicals from acetone extract of Helianthus annuus L. seeds responsible for α-amylase and α-glucosidase inhibition revealed from in vitro and in silico approaches.Methods: Seed extract was qualitatively and quantitatively analysed for the presence of bioactive molecules. In vitro α-amylase and α-glucosidase inhibition assays and kinetics studies for α-glucosidase were done. Thin layer chromatography (TLC) autography of extract was done to screen potent inhibitors and characterized by high-resolution liquid chromatography-mass spectrometry (HR LC-MS). Characterized molecules were further used for in silico studies.Results: Qualitative investigation reveals the presence of flavonoids, glycosides, alkaloids, terpenoids, and steroids. Quantitative analysis for total phenolic content and total flavonoid content of the extract was 0.1±0.005 mg/ml GAE and 0.025±0.003 mg/ml QE respectively. Percent inhibition of α-amylase and α-glucosidase ascertained in presence of extract was 60.42±0.6 and 83.22±0.18 at 0.01 mg while 36.24±0.81 and 37.67±0.15 at 0.005 mg of extracts for both enzymes respectively. Kinetics studies of α-glucosidase inhibition illustrated the non-competitive type of inhibition. TLC autography inhibition patterns were characterized by HR LC-MS. Characterized molecules on docking revealed (6RS)-22-hydroxy-23,24,25,26,27-pentanor-vitamin-D3-6,19-sulfurdioxide-adduct, manoalide and 5β-cholestane-3α,7α,12α,24,25,26-hexol as the best docked molecules with lowest binding energies of-12.5,-11 and-10.2 kcal/mol for α-amylase and-14.2,-11 and-11.2 kcal/mol for α-glucosidase respectively.Conclusion: Results clearly suggested that (6RS)-22-hydroxy-23,24,25,26,27-pentanor-vitamin-D3-6,19-sulfurdioxide-adduct, manoalide and 5β-cholestane-3α,7α,12α,24,25,26-hexol could be considered as lead molecules for the discovery of potent antidiabetic agents. 

scholarly journals Role of Endoplasmic Reticulum Stress in the Anticancer Activity of Natural Compounds

2019 ◽  
Vol 20 (4) ◽  
pp. 961 ◽  
Author(s):  
Patrizia Limonta ◽  
Roberta Moretti ◽  
Monica Marzagalli ◽  
Fabrizio Fontana ◽  
Michela Raimondi ◽  
...  
Keyword(s):  
Endoplasmic Reticulum ◽  
Er Stress ◽  
Anticancer Activity ◽  
Molecular Mechanisms ◽  
Natural Compounds ◽  
New Drugs ◽  
Bioactive Molecules ◽  
Green Tea Polyphenols ◽  
Cell Death Pathways ◽  
Incidence And Mortality

Cancer represents a serious global health problem, and its incidence and mortality are rapidly growing worldwide. One of the main causes of the failure of an anticancer treatment is the development of drug resistance by cancer cells. Therefore, it is necessary to develop new drugs characterized by better pharmacological and toxicological profiles. Natural compounds can represent an optimal collection of bioactive molecules. Many natural compounds have been proven to possess anticancer effects in different types of tumors, but often the molecular mechanisms associated with their cytotoxicity are not completely understood. The endoplasmic reticulum (ER) is an organelle involved in multiple cellular processes. Alteration of ER homeostasis and its appropriate functioning originates a cascade of signaling events known as ER stress response or unfolded protein response (UPR). The UPR pathways involve three different sensors (protein kinase RNA(PKR)-like ER kinase (PERK), inositol requiring enzyme1α (IRE1) and activating transcription factor 6 (ATF6)) residing on the ER membranes. Although the main purpose of UPR is to restore this organelle’s homeostasis, a persistent UPR can trigger cell death pathways such as apoptosis. There is a growing body of evidence showing that ER stress may play a role in the cytotoxicity of many natural compounds. In this review we present an overview of different plant-derived natural compounds, such as curcumin, resveratrol, green tea polyphenols, tocotrienols, and garcinia derivates, that exert their anticancer activity via ER stress modulation in different human cancers.

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