Discovery of novel α-amylase inhibitors using structure-based drug design
Ontology highlight
ABSTRACT:
SUBMITTER: Al-Asri J
PROVIDER: S-EPMC3980051 | biostudies-literature | 2014 Jan
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:ObjectivesDiabetes places a substantial economic burden on countries worldwide. The costs associated with diabetes management, including healthcare services, medications, monitoring equipment, and productivity losses, are substantial. The International Diabetes Federation has estimated that global healthcare expenditures associated with diabetes and its complications exceed hundreds of billions of dollars annually. Therefore, a critical need exists to develop drugs that are highly effective, affordable, and easily accessible to society.MethodsThis study explored the structural modification of 1,4-DHP derivatives to identify specific α-amylase inhibitors, with the aim of developing more effective and accessible drugs for diabetes. We evaluated the activity and binding ability of the designed compounds. In addition, we performed drug-likeness and pharmacokinetic studies on the modified compounds.ResultsEquation (1) had the highest accuracy, on the basis of internal and external assessment parameters, including R2int = 0.852, R2adj = 0.803, Q2cv = 0.731, and R2ext = 0.884. Moreover, the five potent analogs identified through structure-based drug design demonstrated a more favorable interaction than observed for the template or acarbose. Additionally, comprehensive studies on the drug-like properties and pharmacokinetics of the designed compounds supported their oral safety and favorable pharmacokinetic profiles.ConclusionsThe designed analogs show promise for developing new hypoglycemic agents. Their positive attributes and performance suggest that they may potentially serve as candidates for further research in improving treatments for high blood sugar-associated conditions.
| S-EPMC10793175 | biostudies-literature
Project description:Fragment screening is frequently used for hit identification. However, there was no report starting from a small fragment for the development of an anaplastic lymphoma kinase (ALK) inhibitor, despite the number of ALK inhibitors reported. We began our research with the fragment hit F-1 and our subsequent linker design, and its docking analysis yielded novel cis-1,2,2-trisubstituted cyclopropane 1. The fragment information was integrated with a structure-based approach to improve upon the selectivity over tropomyosin receptor kinase A, leading to the potent and highly selective ALK inhibitor, 4-trifluoromethylphenoxy-cis-1,2,2-trisubstituted cyclopropane 12. This work shows that fragments become a powerful tool for both lead generation and optimization, such as the improvement of selectivity, by combining them with a structure-based drug design approach, resulting in the fast and efficient development of a novel, potent, and highly selective compound.
| S-EPMC7745413 | biostudies-literature
Project description:Developing new, more effective antibiotics against resistant Mycobacterium tuberculosis that inhibit its essential proteins is an appealing strategy for combating the global tuberculosis (TB) epidemic. Finding a compound that can target a particular cavity in a protein and interrupt its enzymatic activity is the crucial objective of drug design and discovery. Such a compound is then subjected to different tests, including clinical trials, to study its effectiveness against the pathogen in the host. In recent times, new techniques, which involve computational and analytical methods, enhanced the chances of drug development, as opposed to traditional drug design methods, which are laborious and time-consuming. The computational techniques in drug design have been improved with a new generation of software used to develop and optimize active compounds that can be used in future chemotherapeutic development to combat global tuberculosis resistance. This review provides an overview of the evolution of tuberculosis resistance, existing drug management, and the design of new anti-tuberculosis drugs developed based on the contributions of computational techniques. Also, we show an appraisal of available software and databases on computational drug design with an insight into the application of this software and databases in the development of anti-tubercular drugs. The review features a perspective involving machine learning, artificial intelligence, quantum computing, and CRISPR combination with available computational techniques as a prospective pathway to design new anti-tubercular drugs to combat resistant tuberculosis.
| S-EPMC8703488 | biostudies-literature
Project description:Alzheimer disease and related dementias are major challenges, demanding urgent needs for earliest possible diagnosis to optimize the success rate in finding effective therapeutic interventions. Mounting solid scientific premises point at the core acetylcholine-biosynthesizing cholinergic enzyme, ChAT as a legitimate in vivo target for developing positron emission tomography biomarker for early diagnosis and/or monitoring therapeutic responses in the neurodegenerative dementias. Up-to-date, no PET tracer ligands for ChAT are available. Here we report for the first time a novel hierarchical virtual screening approach on a commercial library of ~300,000 compounds, followed by in vitro screening of the hits by a new High-Throughput ChAT assay. We report detailed pharmacodynamic data for three identified selective novel ChAT ligands with IC50 and K i values ranging from ~7 to 26 µM. In addition, several novel selective inhibitors of the acetylcholine-degrading enzymes, AChE and BuChE were identified, with one of the compounds showing an IC50-value of ~6 µM for AChE. In conclusion, this report provides an excellent starting platform for designing and optimizing potent and selective ChAT ligands, with high potential as PET-imaging probe for early diagnosis of AD, and related dementias, such as Down's syndrome and Lewy body disorders.
| S-EPMC5701137 | biostudies-literature
Project description:Human Epidermal Growth Factor Receptor-1 (EGFR), a transmembrane tyrosine kinase receptor (RTK), has been associated with several types of cancer, including breast, lung, ovarian, and anal cancers. Thus, the receptor was targeted by a variety of therapeutic approaches for cancer treatments. A series of chalcone derivatives are among the most highly potent and selective inhibitors of EGFR described to date. A series of chalcone derivatives were proposed in this study to investigate the intermolecular interactions in the active site utilizing molecular docking and molecular dynamics simulations. After a careful analysis of docking results, compounds 1a and 1d were chosen for molecular dynamics simulation study. Extensive hydrogen bond analysis throughout 7 ns molecular dynamics simulation revealed the ability of compounds 1a and 1d to retain the essential interactions needed for the inhibition, especially MET 93. Finally, MM-GBSA calculations highlight on the capability of the ligands to bind strongly within the active site with binding energies of -44.04 and -56.6 kcal/mol for compounds 1a and 1d, respectively. Compound 1d showed to have a close binding energy with TAK-285 (-66.17 kcal/mol), which indicates a high chance for compound 1d to exhibit inhibitory activity, thus recommending to synthesis it to test its biological activity. It is anticipated that the findings reported here may provide very useful information for designing effective drugs for the treatment of EGFR-related cancer disease.
| S-EPMC6321200 | biostudies-literature
Project description:Therapeutics are currently unavailable for Venezuelan equine encephalitis virus (VEEV), which elicits flu-like symptoms and encephalitis in humans, with an estimated 14% of cases resulting in neurological disease. Here we identify anti-VEEV agents using in silico structure-based-drug-design (SBDD) for the first time, characterising inhibitors that block recognition of VEEV capsid protein (C) by the host importin (IMP) α/β1 nuclear transport proteins. From an initial screen of 1.5 million compounds, followed by in silico refinement and screening for biological activity in vitro, we identified 21 hit compounds which inhibited IMPα/β1:C binding with IC50s as low as 5 µM. Four compounds were found to inhibit nuclear import of C in transfected cells, with one able to reduce VEEV replication at µM concentration, concomitant with reduced C nuclear accumulation in infected cells. Further, this compound was inactive against a mutant VEEV that lacks high affinity IMPα/β1:C interaction, supporting the mode of its antiviral action to be through inhibiting C nuclear localization. This successful application of SBDD paves the way for lead optimization for VEEV antivirals, and is an exciting prospect to identify inhibitors for the many other viral pathogens of significance that require IMPα/β1 in their infectious cycle.
| S-EPMC5735092 | biostudies-literature
Project description:A series of chalcones containing a pyrrolidine moiety were synthesized to examine their in vitro α-amylase and α-glucosidase inhibitory activities, for the treatment of Diabetes mellitus, which is one of the most dangerous and rapidly increasing disorders of today. Compound 3 exhibited an excellent dual inhibitory effect with an IC50 value of 14.61 ± 0.12 μM against α-amylase, and with an IC50: 25.38 ± 2.09 μM against α-glucosidase. The in vitro cytotoxic effects of all compounds against nonsmall lung cancer (A549) and bronchial epithelial normal (BEAS-2B) cell lines were also evaluated. Compound 5 (IC50: 82.20 μM) and compound 8 (IC50: 59.96 μM) showed better cytotoxic activity than cisplatin against A549 (IC50: 84.39 μM) cells. Furthermore, these compounds had no harmful effect on healthy BEAS-2B cells at the determined IC50 values. Moreover, the molecular docking and molecular dynamics simulation analysis revealed that all synthesized compounds exhibited stronger binding affinities toward α-glucosidase and α-amylase compared to the positive control acarbose.
| S-EPMC11904715 | biostudies-literature
Project description:Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological agent of coronavirus disease 2019 (COVID-19), in which the main protease (Mpro) plays an important role in the virus's life cycle. In this work, two representative peptide inhibitors (11a and PF-07321332) were selected, and their interaction mechanisms of non-covalently bound with Mpro were firstly investigated by means of molecular dynamical simulation. Then, using the fragment-based drug design method, some fragments from the existing SARS-CoV and SARS-CoV-2 inhibitors were selected to replace the original P2 and P3 fragments, resulting in some new molecules. Among them, two molecules (O-74 and N-98) were confirmed by molecular docking and molecular dynamics simulation, and ADMET properties prediction was employed for further verification. The results shown that they presented excellent activity and physicochemical properties, and had the potential to be new inhibitors for SARS-CoV-2 main protease.
| S-EPMC9837207 | biostudies-literature
Project description:Alpha-amylase is a known target for type II diabetes. Therefore, it is of interest to design α-amylase inhibitors based on hydrazone scaffold. The structure of these hybrids was confirmed by spectroscopic analysis (IR, 1H-and 13C NMR). All the compounds have potential inhibitory properties as shown by in vitro α-amylase inhibition activity. The compound 5-((1Z,3Z)-3-(benzo[d][1,3]dioxol-5-yl)-3-((2-chloropyridin-3- yl)imino)prop-1-en-1-yl)-2-(difluoromethoxy)phenol(4a) in 100 µg/mL concentration showed a high inhibition of 85.23%. In vitro α-amylase inhibition was further supported by docking studies of compound against the active site of pig pancreatic α-amylase (PDB ID: 3L2M). Docking studies revealed that the bonding interactions found between the compound and human pancreatic α-amylase are similar to those responsible for α-amylase inhibition by acarbose.
| S-EPMC6704331 | biostudies-literature
Project description:The ATPase subunit of DNA gyrase B is an attractive antibacterial target due to high conservation across bacteria and the essential role it plays in DNA replication. A novel class of pyrazolopyridone inhibitors was discovered by optimizing a fragment screening hit scaffold using structure guided design. These inhibitors show potent Gram-positive antibacterial activity and low resistance incidence against clinically important pathogens.
| S-EPMC4834655 | biostudies-literature