Docking and Molecular Dynamics Calculations of Pyrrolidinone Analog MMK16 Bound to COX and LOX Enzymes

Explainable artificial intelligence-assisted virtual screening and bioinformatics approaches for effective bioactivity prediction of phenolic cyclooxygenase-2 (COX-2) inhibitors using PubChem molecular fingerprints

Cyclooxygenase-2 (COX-2) inhibitors are nonsteroidal anti-inflammatory drugs that treat inflammation, pain and fever. This study determined the interaction mechanisms of COX-2 inhibitors and the molecular properties needed to design new drug candidates. Using machine learning and explainable AI methods, the inhibition activity of 1488 molecules was modelled, and essential properties were identified. These properties included aromatic rings, nitrogen-containing functional groups and aliphatic hydrocarbons. They affected the water solubility, hydrophobicity and binding affinity of COX-2 inhibitors. The binding mode, stability and ADME properties of 16 ligands bound to the Cyclooxygenase active site of COX-2 were investigated by molecular docking, molecular dynamics simulation and MM-GBSA analysis. The results showed that ligand 339,222 was the most stable and effective COX-2 inhibitor. It inhibited prostaglandin synthesis by disrupting the protein conformation of COX-2. It had good ADME properties and high clinical potential. This study demonstrated the potential of machine learning and bioinformatics methods in discovering COX-2 inhibitors.

Synthesis, Anti-Inflammatory Activity and Molecular Docking Studies of 1,4,5,6-Tetrahydropyrimidine-2-Carboxamides

Background: Nonsteroidal anti-inflammatory drugs (NSAIDs) are among the most commonly used drugs in the world. The widespread use of NSAIDs is associated with a number of serious side effects and complications observed for both selective and non-selective COX inhibitors. Therefore, the search for new COX inhibitors, which along with their effectiveness will have minimal side effects, is a very important and urgent task. Methods: This work studied the synthesis of new 1,4,5,6-tetrahydropyrimidine-2-carboxamides based on the reaction of 2-morpholin-4-yl-N-(het)aryl-2-thioxoacetamides with 1,3-diaminopropane. All obtained compounds were tested for anti-inflammatory activity in vitro and in silico conditions. All synthesized 1,4,5,6-tetrahydropyrimidine-2-carboxamides were tested for influence on the course of the exudative phase of the inflammatory process based on the carrageenan model of paw edema of laboratory nonlinear heterosexual white rats weighing 220-250 g, using Diclofenac as a reference. Optimization of the geometry of the studied structures and molecular docking was carried out using the ArgusLab 4.0.1 software package. Results: The target products were obtained with yields of 71-98% and easily isolated from the reaction mixture. The best anti-inflammatory activity was found in N-(4-chlorophenyl)-1,4,5,6-tetrahydropyrimidine-2-carboxamide and in N-[4-chloro-3-(trifluoromethyl)phenyl]-1,4,5,6-tetrahydropyrimidine-2-carboxamide, suppression of the inflammatory response was 46.7 and 46.4%, respectively. The results of molecular docking with COX-1 and COX-2 enzymes were in good agreement with the experimental data, R2 ˃ 0.92 and R2 ˃ 0.83, respectively. Conclusion: The compounds under study were shown to be promising as potential anti-inflammatory agents.

Application of per-residue energy decomposition to identify the set of amino acids critical for in silico prediction of COX-2 inhibitory activity

The enormous magnitude of scientific research carried out in the field of NSAIDs and cyclooxygenases (COXs) is known. They are crucial in pain management. COX-2 inhibitors have evolved over the years; from traditional NSAIDs to isoform-specific. The present study is aimed to identify a cluster of amino acids in the catalytic site whose energy contribution can better explain COX-2 inhibitory activity accurately than the binding energy of the whole protein. Initially, MD simulations (25 ns) and MM-PBSA calculations were performed for 8 diarylheterocyclic inhibitors. Per-residue energy decomposition studies were carried out to elucidate the energy contribution of each amino acid, and their correlation with COX-2 inhibitory activity was enumerated. A cluster of catalytic amino acids whose free energy sum has a high correlation with biological data was identified. The cluster of Gln178, Ser339, Tyr341, Arg499, Phe504, Val509 and Ala513 showed the correlation of -0.60. Further, the study was extended to a total of 26 COX-2 inhibitors belonging to different classes to validate the applicability of the cluster of amino acids identified. Results clearly suggest that the cluster of amino acids identified provide accurate screening method, and can be applied to predict COX-2 inhibitory activity of small molecules.

Insights into the inhibitory mechanism and molecular interaction of novel alkaloids from Beilschmiedia glabra with lipoxygenase and acetylcholinesterase

In this study, the mechanism underlying acetylcholinesterase (AChE) and 5-lipoxygenase (LOX) inhibition by two novel alkaloids, beilschglabrine A and beilschglabrine B, as well as their interaction footprints on the binding pockets were investigated. The results showed that beilschglabrine A and beilschglabrine B inhibit both AChE and LOX in a competitive manner by binding to their active sites thereby interfering with substrate access. The interaction of the alkaloids with the enzymes was favorable and stable with low binding energy values which correlate well with their IC[Formula: see text]. The depicted molecular interaction, structure-energetic pattern and binding conformations confirmed that beilschglabrine A is more potent than beilschglabrine B. The differences in the binding pose and potency of the alkaloids is occasioned by an extra methyl moiety on beilschglabrine B. The chemical scaffold of the alkaloids respected Lipinski’s rule of five and may be relevant in the development of new anti-inflammatory and anti-neurodegenerative disease drugs acting via AChE and LOX inhibition.

Isolation of Compounds from Sargassum wightii by GCMS and the Molecular Docking against Anti-Inflammatory Marker COX2

The study focused on the molecular docking of GC-MS isolated compounds from theSargassum wightiiagainst inflammatory marker Cycloxigenase-2 (COX2). Seven compounds isolated by GC-MS were tested for their anti-inflammatory action using insilico analysis. The crystal structure obtained from the protein data bank was docked against seven compounds and the glide score as well as glide energy were determined using Schrödinger Maestro software (version 2013.1). The results of molecular docking showed that out of the seven bioactive compounds tested, methyl salicylate, benzoic acid, 2-hydroxy-,ethyl ester, diethyl phthalate, hexadecanoic acid, ethyl ester and (E) -9-octadecenoic acid ethyl ester were effectively inhibited the COX2 protein. The ADME properties of the compounds analyzed using Qikprop version 3.6 software of Schrodinger suite and the results showed that all the compounds were biologically active and the scores were within the acceptable range. This study revealed that the possibility of using these compounds against COX2 to treat inflammation.

Alditols and monosaccharides from sorghum vinegar can attenuate platelet aggregation by inhibiting cyclooxygenase-1 and thromboxane-A2 synthase

ETHNOPHARMACOLOGICAL RELEVANCE

Vinegar has been used as both a common seasoning and a traditional Chinese medicine. Sorghum vinegar is an excellent source of physiological substances with multiple health benefits.

AIM OF THIS STUDY

To evaluate the antiplatelet aggregation activity of alditols and monosaccharides extracted from sorghum vinegar and analysis its mechanism.

MATERIALS AND METHODS

Alditol and monosaccharide extract (AME) from sorghum vinegar was first evaluated for antiplatelet activity using the turbidimetric method. Blood was collected from healthy volunteer donors. The platelet aggregation was induced by arachidonic acid (AA), collagen, adenosine diphosphate (ADP) and thrombin in vitro. AME was divided into three experimental groups with the concentration were 0.10, 0.25 and 0.50 mg/mL. In order to determine the inhibitory activity of AME on COX1, TXS and TXA2 production experiments were conducted using the COX1, TXS and TXB2 EIA kit. Computational docking was used to find the docking pose of monosaccharides and alditols with COX1.

RESULTS

AME showed significant induction of antiplatelet activity by arachidonic acid (AA), collagen, adenosine diphosphate (ADP) and thrombin in a concentration-dependent manner (p<0.05). AME (0.50 mg/mL) reduced the AA-induced aggregation rate to 10.35%±0.46%, which was comparable to acetylsalicylic acid (aspirin, ASA) (0.50 mg/mL, 6.35%±0.58%), a medical standard. Furthermore, AME strongly inhibited cyclooxygenase-1 (COX1) and thromboxane-A2 synthase (TXS), and subsequently attenuated thromboxane-A2 (TXA2) production. These findings indicated that AME attenuates platelet aggregation through the AA metabolism pathway. Computational docking showed that alditols (L-erythritol, L-arabitol, xylitol and D-sorbitol), monosaccharides (D-glucopyranose, D-fructofuranonse, D-xylopyranose, D-galactopyranose and D-ribose), ethyl glucoside and 3,4-(methylenedioxy) mandelic acid could dock directly into the active site of COX1.

CONCLUSION

Alditols and monosaccharides from sorghum vinegar inhibit multiple steps in the platelet aggregation pathway, and may be beneficial for the treatment of cardiovascular diseases.