Navigating into the Chemical Space of Monoamine Oxidase Inhibitors by Artificial Intelligence and Cheminformatics Approach

In silico study to recognize novel angiotensin-converting-enzyme-I inhibitors by 2D-QSAR and constraint-based molecular simulations

Cardiovascular diseases (CVD) such as heart failure, stroke, and hypertension affect 64.3 million people worldwide and are responsible for 30% of all deaths. Primary inhibition of the angiotensin-converting enzyme (ACE) is significant in the management of CVD. In the present study, the genetic algorithm-multiple linear regressions (GA-MLR) method is used to generate highly predictive and statistically significant (R2 = 0.70-0.75, Q2LOO=0.67-0.73, Q2LMO=0.66-0.72, CCCex=0.70-0.78) quantitative structure-activity relationships (QSAR) models conferring to OECD requirements using a dataset of 255 structurally diverse and experimentally validated ACE inhibitors. The models contain simply illustratable Padel, Estate, and PyDescriptors that correlate structural scaffold requisite for ACE inhibition. Also, constraint-based molecular docking reveals an interaction profile between ligands and enzymes which is then correlated with the essential structural features associated with the QSAR models. The QSAR-based virtual screening was utilized to find novel lead molecules from a designed database of 102 thiadiazole derivatives. The Applicability domain (AD), Molecular Docking, Molecular dynamics, and ADMET analysis suggest two compound D24 and D40 are inflexibly linked to the protein binding site and follows drug-likeness properties.Communicated by Ramaswamy H. Sarma.

In Vitro Human Monoamine Oxidase Inhibition and Human Dopamine D4 Receptor Antagonist Effect of Natural Flavonoids for Neuroprotection

Natural flavone and isoflavone analogs such as 3',4',7-trihydroxyflavone (1), 3',4',7-trihydroxyisoflavone (2), and calycosin (3) possess significant neuroprotective activity in Alzheimer's and Parkinson's disease. This study highlights the in vitro human monoamine oxidase (hMAO) inhibitory potential and functional effect of those natural flavonoids at dopamine and serotonin receptors for their possible role in neuroprotection. In vitro hMAO inhibition and enzyme kinetics studies were performed using a chemiluminescent assay. The functional effect of three natural flavonoids on dopamine and serotonin receptors was tested via cell-based functional assays followed by a molecular docking simulation to predict interactions between a compound and the binding site of the target protein. A forced swimming test was performed in the male C57BL/6 mouse model. Results of in vitro chemiluminescent assays and enzyme kinetics depicted 1 as a competitive inhibitor of hMAO-A with promising potency (IC50 value: 7.57 ± 0.14 μM) and 3 as a competitive inhibitor of hMAO-B with an IC50 value of 7.19 ± 0.32 μM. Likewise, GPCR functional assays in transfected cells showed 1 as a good hD4R antagonist. In docking analysis, these active flavonoids interacted with a determinant-interacting residue via hydrophilic and hydrophobic interactions, with low docking scores comparable to reference ligands. The post-oral administration of 1 to male C57BL/6 mice did not reduce the immobility time in the forced swimming test. The results of this study suggest that 1 and 3 may serve as effective regulators of the aminergic system via hMAO inhibition and the hD4R antagonist effect, respectively, for neuroprotection. The route of administration should be considered.

Fragment-based structural exploration and chemico-biological interaction study of HDAC3 inhibitors through non-linear pattern recognition, chemical space, and binding mode of interaction analysis

HDAC3 is an emerging target for the identification and discovery of novel drug candidates against several disease conditions including cancer. Here, a fragment-based non-linear machine learning (ML) method along with chemical space exploration followed by a structure-based binding mode of interaction analysis study was carried out on some HDAC3 inhibitors to obtain the key structural features modulating HDAC3 inhibition. Both the ML and chemical space analysis identified several physicochemical and structural properties namely lipophilicity, polar and relative polar surface area, arylcarboxamide moiety, bulky fused aromatic group, n-alkyl, and cinnamoyl moieties, the higher number of oxygen atoms, π-electrons for the substituted tetrahydrofuronaphthodioxolone moiety favorable for higher HDAC3 inhibition. Moreover, hydrogen bond forming capabilities, the length and substitution position of the linker moiety, the importance of phenyl ring in the linker motif, the contribution of heterocyclic cap moieties for effective inhibitor binding at the HDAC3 catalytic site that correspondingly affects the HDAC3 inhibitory potency. Again, macrocyclic ring structure and cyclohexyl cap moiety are responsible for lower HDAC3 inhibition. The MD simulation study of selected compounds explained strong binding patterns at the HDAC3 active site as evidenced by the lower RMSD and RMSF values. Nevertheless, it also explained the importance of the crucial structural fragments derived from the fragment-based analysis during ligand-enzyme interactions. Therefore, the outcomes of this current structural analysis will be a useful tool for fragment-based drug discovery of effective HDAC3 inhibitors for clinical therapeutics in the future.Communicated by Ramaswamy H. Sarma.

An efficient method to access spiro pseudoindoxyl ketones: evaluation of indoxyl and their N-benzylated derivatives for inhibition of the activity of monoamine oxidases

A simple, metal-free approach was developed to obtain novel pseudoindoxyl derivatives. The reaction was mediated by tBuOK on tetrahydrocarbazole 8 in dimethyl sulfoxide (DMSO) at room temperature through the hydroxylation of the indole double bond and a subsequent pinacol-type rearrangement. Spiro pseudoindoxyl compounds and their N-benzylated derivatives were assessed for their inhibitory activities against monoamine oxidase (MAO) enzymes. Based on half-maximal inhibitory concentration (IC50) values, 13 compounds were found to have higher inhibitory activity against MAO-B than against MAO-A. With regard to MAO-B inhibition, 11f showed the best inhibitory activity, with an IC50 value of 1.44 μM, followed by 11h (IC50 = 1.60 μM), 11j (IC50 = 2.78 μM), 11d (IC50 = 2.81 μM), and 11i (IC50 = 3.02 μM). Compound 11f was a competitive inhibitor with a Ki value of 0.51 ± 0.023 μM. In a reversibility experiment using dialysis, 11f showed effective recovery of MAO-B inhibition similar to that of safinamide. These experiments suggested that 11f was a potent, reversible, and competitive inhibitor of MAO-B activity.

Exploration of a new class of monoamine oxidase B inhibitors by assembling benzyloxy pharmacophore on halogenated chalcones

Eight derivatives of benzyloxy-derived halogenated chalcones (BB1-BB8) were synthesized and tested for their ability to inhibit monoamine oxidases (MAOs). MAO-A was less efficiently inhibited by all compounds than MAO-B. Additionally, the majority of the compounds displayed significant MAO-B inhibitory activities at 1 μM with residual activities of less than 50%. With an IC50 value of 0.062 μM, compound BB4 was the most effective in inhibiting MAO-B, followed by compound BB2 (IC50  = 0.093 μM). The lead molecules showed good activity than the reference MAO-B inhibitors (Lazabemide IC50  = 0.11 μM and Pargyline Pargyline IC50  = 0.14). The high selectivity index (SI) values for MAO-B were observed in compounds BB2 and BB4 (430.108 and 645.161, respectively). Kinetics and reversibility experiments revealed that BB2 and BB4 were reversible competitive MAO-B inhibitors with Ki values of 0.030 ± 0.014 and 0.011 ± 0.005 μM, respectively. Swiss target prediction confirmed the high probability in the targets of MAO-B for both compounds. Hypothetical binding mode revealed that the BB2 or BB4 is similarly oriented to the binding cavity of MAO-B. Based on the modelling results, BB4 showed a stable confirmation during the dynamic simulation. From these results, it was concluded that BB2 and BB4 were potent selective reversible MAO-B inhibitors and they can be considered drug candidates for treating related neurodegenerative diseases such as Parkinson's disease.

New Insights on the Activity and Selectivity of MAO-B Inhibitors through In Silico Methods

To facilitate the identification of novel MAO-B inhibitors, we elaborated a consolidated computational approach, including a pharmacophoric atom-based 3D quantitative structure-activity relationship (QSAR) model, activity cliffs, fingerprint, and molecular docking analysis on a dataset of 126 molecules. An AAHR.2 hypothesis with two hydrogen bond acceptors (A), one hydrophobic (H), and one aromatic ring (R) supplied a statistically significant 3D QSAR model reflected by the parameters: R² = 0.900 (training set); Q² = 0.774 and Pearson's R = 0.884 (test set), stability s = 0.736. Hydrophobic and electron-withdrawing fields portrayed the relationships between structural characteristics and inhibitory activity. The quinolin-2-one scaffold has a key role in selectivity towards MAO-B with an AUC of 0.962, as retrieved by ECFP4 analysis. Two activity cliffs showing meaningful potency variation in the MAO-B chemical space were observed. The docking study revealed interactions with crucial residues TYR:435, TYR:326, CYS:172, and GLN:206 responsible for MAO-B activity. Molecular docking is in consensus with and complementary to pharmacophoric 3D QSAR, ECFP4, and MM-GBSA analysis. The computational scenario provided here will assist chemists in quickly designing and predicting new potent and selective candidates as MAO-B inhibitors for MAO-B-driven diseases. This approach can also be used to identify MAO-B inhibitors from other libraries or screen top molecules for other targets involved in suitable diseases.

Identification of new small molecule monoamine oxidase-B inhibitors through pharmacophore-based virtual screening, molecular docking and molecular dynamics simulation studies

The discovery of a safe and efficacious drug is a complex, time-consuming, and expensive process. Computational methodologies driven by cheminformatics tools play a central role in the high-throughput lead discovery and optimization process especially when the structure of the biological target is known. Monoamine oxidases are the membrane-bound FAD-containing enzymes and the isoform monoamine oxidase-B (MAO-B) is an attractive target for treating diseases like Alzheimer's disease, Parkinson's disease, glioma, etc. In the current study, we have used a pharmacophore-based virtual screening technique for the identification of new small molecule MAO-B inhibitors. Safinamide was used for building a pharmacophore model and the developed model was used to probe the ZINC database for potential hits. The obtained hits were filtered against drug-likeness and PAINS. Out of the hit's library, two compounds ZINC02181408, ZINC08853942 (most active), and ZINC53327382 (least active) were further subjected to molecular docking and dynamics simulation studies to assess their virtual binding affinities and stability of the resultant protein-ligand complex. The docking studies revealed that active ligands were well accommodated within the active site of MAO-B and interacted with both substrate and entrance cavity residues. MD simulation studies unveiled additional hydrogen bond interactions with the substrate cavity residues, Tyr398 and Tyr435 that are crucial for the catalytic role of MAO-B. Moreover, the predicted ADMET parameters suggest that the compounds ZINC08853942 and ZINC02181408 are suitable for CNS penetration. Thus, the attempted computational campaign yielded two potential MAO-B inhibitors that merit further experimental investigation.Communicated by Ramaswamy H. Sarma.

Interactions of coumarin derivatives with monoamine oxidase biomarkers: In silico approach

A list of coumarin derivatives (A-P) were investigated in this work for recognizing their reactivity features and their functions towards the monoamine oxidase (MAO) enzyme biomarkers. In this regard, the models showed that he additional of molecular groups to the original scaffold of coumarin could significantly change the reactivity features leading to various tendency for contributing to reactions with other substances. In this case, were varied based on the obtained values of chemical hardness and softness parameters. Subsequently, formations of interacting ligand-target complexes indicated the coumarin derivatives could work as selective substances for interacting with each of MAOA (D) and MAOB (L) enzyme biomarkers, in which a common substance (E) was also observed for formation of interacting complexes with both of MAOA and MAOB targets. As a consequence, the models of coumarin were seen suitable for interacting with the MAO enzyme biomarkers with the purposes of detection and medication. All required information of this work were obtained in the in silico medium.

Replacement of Chalcone-Ethers with Chalcone-Thioethers as Potent and Highly Selective Monoamine Oxidase-B Inhibitors and Their Protein-Ligand Interactions

To develop new potent and highly selective MAO-B inhibitors from chalcone-thioethers, eleven chalcones-thioethers were synthesized and their monoamine oxidase (MAO) inhibition, kinetics, reversibility, and cytotoxicity of lead compounds were analyzed. Molecular dynamics were carried out to investigate the interactions. Compound TM8 showed potent inhibitory activity against MAO-B, with an IC₅₀ value of 0.010 µM, followed by TM1, TM2, TM7, and TM10 (IC₅₀ = 0.017, 0.021, 0.023, and 0.026 µM, respectively). Interestingly, TM8 had an extremely high selectivity index (SI; 4860) for MAO-B. Reversibility and kinetic experiments showed that TM8 and TM1 were reversible and competitive inhibitors of MAO-B with K_i values of 0.0031 ± 0.0013 and 0.011± 0.001 µM, respectively. Both TM1 and TM8 were non-toxic to Vero cells with IC₅₀ values of 241.8 and 116.3 µg/mL (i.e., 947.7 and 402.4 µM), respectively, and at these IC₅₀ values, both significantly reduced reactive oxygen species (ROS) levels. TM1 and TM8 showed high blood-brain barrier permeabilities in the parallel artificial membrane permeability assay. Molecular dynamics studies were conducted to investigate interactions between TM1 and TM8 and the active site of MAO-B. Conclusively, TM8 and TM1 are potent and highly selective MAO-B inhibitors with little toxicity and good ROS scavenging abilities and it is suggested that both are attractive prospective candidates for the treatment of neurological disorders.