Browse
Submit Data
Databases
API
Help

Dataset Information

11 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Theoretical Studies on the Molecular Properties, Toxicity, and Biological Efficacy of 21 New Chemical Entities.

ABSTRACT: New chemical entities (NCEs) such as small molecules and antibody-drug conjugates have strong binding affinity for biological targets, which provide deep insights into structure-specific interactions for the design of future drugs. As structures of drugs increase in complexity, the importance of computational predictions comes into sharp focus. Knowledge of various computational tools enables us to predict the molecular properties, toxicity, and biological efficacy of the drugs and help the medicinal chemists to discover new drugs more efficiently. Newly approved drugs have higher affinities for proteins and nucleic acids and are applied for the treatment of human diseases. We have carried out the computational studies of 21 such NCEs, specifically small molecules and antibody-drug conjugates, and studied the biological efficacy of these drugs. Their bioactivity score and molecular and pharmacokinetic properties were evaluated using online computer software programs, viz., Molinspiration and Osiris Property Explorer. The SwissTargetPrediction tool was used for the efficient prediction of protein targets for the NCEs. The results indicated higher stability for the drug complexes due to a larger HOMO-LUMO gap. A high electrophilicity index reflects good electrophilic behavior and high reactivity of the drugs. Lipinski's ''rule of five'' indicated that most of the drug complexes are likely to be orally active. These drugs also showed non-mutagenic, non-tumorigenic, non-irritant, and non-effective reproductive behavior. We hope that these studies will provide an insight into molecular recognition and definitely help the medicinal chemists to design new drugs in future.

SUBMITTER: Srivastava R

PROVIDER: S-EPMC8482469 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Chemical Entities of Biological Interest: an update.

Project description:Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds. The molecular entities in question are either natural products or synthetic products used to intervene in the processes of living organisms. Genome-encoded macromolecules (nucleic acids, proteins and peptides derived from proteins by cleavage) are not as a rule included in ChEBI. In addition to molecular entities, ChEBI contains groups (parts of molecular entities) and classes of entities. ChEBI includes an ontological classification, whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified. ChEBI is available online at http://www.ebi.ac.uk/chebi/. This article reports on new features in ChEBI since the last NAR report in 2007, including substructure and similarity searching, a submission tool for authoring of ChEBI datasets by the community and a 30-fold increase in the number of chemical structures stored in ChEBI.

| S-EPMC2808869 | biostudies-literature

ChEBI: a database and ontology for chemical entities of biological interest.

| S-EPMC2238832 | biostudies-literature

The Chemical and Biological Properties of Propolis

Project description:The term propolis comes from two Greek words, pro (which means for or in defence of) and polis (which means the city); thus, propolis means in defence of the city or beehive. Propolis is a sticky resinous substance, which is gathered from buds and the bark of trees. It is also known as “bee glue” as bees use it to cover surfaces, seal holes and close gaps in their hives, thus providing a sterile environment that protects them from microbes and spore-producing organisms, including fungi and molds. It can be considered to be a potent chemical weapon against bacteria, viruses, and other pathogenic microorganisms that may invade the bee colony. Also, bees use propolis as an embalming substance, to mummify invaders such as other insects, that have been killed and are too heavy to remove from the colony. Thus, propolis is important for bee health but it also has activity against many human diseases. It is a powerful anti-oxidant and can modulate the activity of reactive oxygen species within the human body. The most studied aspect of propolis is its anti-bacterial activity, which is almost always present at a moderate to high level depending on the exact type of propolis. It is in general more active against Gram positive than Gram negative bacteria, but activity against Gram negative bacteria has been observed. Propolis has been found to be active against a range of viruses and also is almost always active against protozoa such as Tryanosoma brucei and Leishmania donovani. Propolis also shows activity against cardiovascular diseases and diabetes and has immunomodulatory effects. Anti-cancer activity has also been observed. In summary, propolis is remarkable for its range of biological activities and for the variety of its chemical composition. It may be of great importance both to bees and humans.

| S-EPMC7123330 | biostudies-literature

Experimentally Validated Pharmacoinformatics Approach to Predict hERG Inhibition Potential of New Chemical Entities.

Project description:The hERG (human ether-a-go-go-related gene) encoded potassium ion (K+) channel plays a major role in cardiac repolarization. Drug-induced blockade of hERG has been a major cause of potentially lethal ventricular tachycardia termed Torsades de Pointes (TdPs). Therefore, we presented a pharmacoinformatics strategy using combined ligand and structure based models for the prediction of hERG inhibition potential (IC50) of new chemical entities (NCEs) during early stages of drug design and development. Integrated GRid-INdependent Descriptor (GRIND) models, and lipophilic efficiency (LipE), ligand efficiency (LE) guided template selection for the structure based pharmacophore models have been used for virtual screening and subsequent hERG activity (pIC50) prediction of identified hits. Finally selected two hits were experimentally evaluated for hERG inhibition potential (pIC50) using whole cell patch clamp assay. Overall, our results demonstrate a difference of less than ±1.6 log unit between experimentally determined and predicted hERG inhibition potential (IC50) of the selected hits. This revealed predictive ability and robustness of our models and could help in correctly rank the potency order (lower ?M to higher nM range) against hERG.

| S-EPMC6176658 | biostudies-literature

A new derivative of acetylsalicylic acid and carnosine: synthesis, physical and chemical properties, biological activity.

Project description:PurposeThe aim of this study was to create and assess biological activity of a new compound based on carnosine and acetylsalicylic acid (ASA) that will comprise antioxidant effect with antiplatelet activity, while simultaneously preventing side effects on the gastrointestinal tract.MethodsSalicyl-carnosine (SC) was synthesized by condensation of ASA and carnosine. Antioxidant activity was determined by spectrophotometric and chemiluminescence methods. Antiplatelet activity was carried out by the light transmission-aggregometry method using the inductor ADP. Chronic gastric ulcer in rats was modeled using glacial acetic acid.ResultsUsing SOD-like activity, iron-induced chemiluminescence, BaSO4-activated respiratory burst, and evaluation of red blood cell structure stabilization during oxidative damage induced by sodium hypochlorite, it was shown that SC possesses antioxidant activity analogous, or better, than that of carnosine. Antiplatelet activity of SC was evaluated in the blood of healthy individuals, and was also shown to be comparable to, or exceeding that of ASA. Also SC demonstrates high resistance to hydrolysis by tissue and serum carnosinases. Most importantly, it was shown that SC has protected the gastric mucosa against the formation of stomach ulcerative lesions and promoted their epithelization, therefore overcoming the undesirable inherent side effects of ASA.ConclusionsSC preserves pharmacologically significant properties of ASA and carnosine while retaining an anti-ulcer activity and resistance to the carnosinase hydrolysis at the same time. These properties are particularly promising for the potential development of new anti-inflammatory and antithrombotic drugs. Graphical abstract .

| S-EPMC7214588 | biostudies-literature

Pharmacophore hybridization and nanoscale assembly to discover new self-delivering lysosomotropic chemical entities for cancer therapy

Project description:Cancer lysosome is a potential target for cancer therapy. We designed and prepared a type of single-drug nanoparticles. These nanoparticles can specifically accumulate in lysosomes when entering cancer cells and are dissociated into small molecules. The small molecules not only act as lysosomotropic detergents to induce lysosomal membrane permeabilization directly, but also act as lysosomomotropic alkalizers to inhibit autophagy. In the meanwhile, these nanoparticles also show a strong proton-sponging effect and induce lysosomal dysfunction. As a result, the nanoparticles exhibit good antiproliferative activity in vitro. These single-drug nanoparticles also demonstrate excellent pharmacokinetic and toxicological profiles and dramatic antitumour efficacy in vivo. In addition, they are able to encapsulate and deliver additional drugs to tumour sites and are thus promising agents for autophagy inhibition-based combination therapy. Given their transdisciplinary advantages, these nanoparticles have enormous potential to improve cancer therapy.

2020-07-14 | GSE154323 | GEO

Chemical and biological studies on Cichorium intybus L.

Project description:Cichorium intybus L. (Asteraceae family) is a world-wide grown plant known as chicory. In traditional medicine, this plant is used as diuretic, anti-inflammatory, digestive, cardiotonic and liver tonic. Chromatographic purification of the supercritical fluid extract of aerial parts of C. intybus on silica gel column led to isolation of three compounds: new compound, 28?-hydroxytaraxasterol (I), and two known compounds usnic acid (II) and ?-sitosterol (III). Purification of the ethanolic extract of aerial parts of this plant on silica gel column chromatography yielded four compounds: 1,3-dioleylglycerate (IV), sitoindoside II (V), 11?-13-dihydrolactucin (VI) and ?-sitosterol-3-O-glucoside (VII). The structures of the isolated compounds were determined by their 1D, 2D NMR and MS spectral data. All the fractions and isolated compounds were tested for cannabinoid and opioid receptor binding, as well as antibacterial, antifungal and antimalarial activities. Compound I showed moderate activity (60.5% displacement) towards CB1 receptor.

| S-EPMC5736470 | biostudies-literature

Chemical and biological studies of nakiterpiosin and nakiterpiosinone.

Project description:Nakiterpiosin and nakiterpiosinone are two related C-nor-D-homosteroids isolated from the sponge Terpios hoshinota that show promise as anticancer agents. We have previously described the asymmetric synthesis and revision of the relative configuration of nakiterpiosin. We now provide detailed information on the stereochemical analysis that supports our structure revision and the synthesis of the originally proposed and revised nakiterpiosin. In addition, we herein describe a refined approach for the synthesis of nakiterpiosin, the first synthesis of nakiterpiosinone, and preliminary mechanistic studies of nakiterpiosin's action in mammalian cells. Cells treated with nakiterpiosin exhibit compromised formation of the primary cilium, an organelle that functions as an assembly point for components of the Hedgehog signal transduction pathway. We provide evidence that the biological effects exhibited by nakiterpiosin are mechanistically distinct from those of well-established antimitotic agents such as taxol. Nakiterpiosin may be useful as an anticancer agent in those tumors resistant to existing antimitotic agents and those dependent on Hedgehog pathway responses for growth.

| S-EPMC2805047 | biostudies-literature

Development of Chemical Entities Endowed with Potent Fast-Killing Properties against <i>Plasmodium falciparum</i> Malaria Parasites.

Project description:One of the attractive properties of artemisinins is their extremely fast-killing capability, quickly relieving malaria symptoms. Nevertheless, the unique benefits of these medicines are now compromised by the prolonged parasite clearance times and the increasing frequency of treatment failures, attributed to the increased tolerance of Plasmodium falciparum to artemisinin. This emerging artemisinin resistance threatens to undermine the effectiveness of antimalarial combination therapies. Herein, we describe the medicinal chemistry efforts focused on a cGMP-dependent protein kinase (PKG) inhibitor scaffold, leading to the identification of novel chemical entities with very potent, similar to artemisinins, fast-killing potency against asexual blood stages that cause disease, and activity against gametocyte activation that is required for transmission. Furthermore, we confirm that selective PKG inhibitors have a slow speed of kill, while chemoproteomic analysis suggests for the first time serine/arginine protein kinase 2 (SRPK2) targeting as a novel strategy for developing antimalarial compounds with extremely fast-killing properties.

| S-EPMC6816013 | biostudies-literature

Theobromacacao Criollo var. Beans: Biological Properties and Chemical Profile.

Project description:Theobroma cacao provides precious products such as polyphenol-rich beans that are useful for nutraceutical purposes. The geographical area may influence the chemical composition of raw cocoa beans in terms of the polyphenols and biological qualities of the products. This work aimed to investigate the biological properties and the chemical composition of two different samples of Criollo var. cocoa raw beans coming from two areas (Indonesia; Peru). Beans underwent biphasic extraction obtaining lipophilic and hydroalcoholic extracts. The extracts were tested for antiradical, antimutagenic, and antigenotoxic effects. Cell viability inhibition toward breast, gastric/esophageal colorectal adenocarcinoma, and hepatoblastoma human cell lines was evaluated. Extracts were chemically investigated through UV-Vis spectroscopy and ultra-high-pressure liquid chromatography electrospray ionization quadrupole time-of-flight mass spectrometry (UHPLC-ESI-QqTOF MS/MS). Results showed that the Indonesian bean hydroalcoholic extracts were able to scavenge 2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS) cation radical better than the Peruvian hydroalcoholic extracts (ECs50: 72.63 vs. 322.20 μg/mL). Extracts showed antimutagenic and antigenotoxic activity. The viability inhibitory effect on breast and hepatic cancer cells was reached only for the Indonesian hydroalcoholic extracts at hundreds of μg/mL. Phenylpropenoyl-L-amino acids, hydroxycinnamoyl aminoacids conjugates, and procyanidin compounds were found mainly in the hydroalcoholic extracts, whereas fatty acids and lyso-phospholipids were found mainly in lipophilic fractions. Fatty acid and (epi)catechins appeared to be affected by different environmental conditions of the geographical areas.

| S-EPMC8001065 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data