Structural insights into ligand binding features of dual FABP4/5 inhibitors by molecular dynamics simulations

Adipocyte fatty acid binding protein 4 (FABP4) inhibitors. An update from 2017 to early 2022

The fatty acid binding protein 4 (FABP4) is a protein predominantly expressed in macrophages and adipose tissue, where it regulates fatty acids storage and lipolysis and is an essential mediator of inflammation. Small molecule inhibitors of FABP4 have attracted interest following the recent publications of beneficial pharmacological effects of these compounds for the treatment of metabolic syndrome and, more recently, for other pathologies. Since the synthesis of the BMS309403, one of the first selective and effective FABP4 inhibitors, hundreds of other inhibitors have been synthesized (i.e., derivatives of niacin, quinoxaline, aryl-quinoline, bicyclic pyridine, urea, aromatic compounds and other novel heterocyclic compounds). This review updates the recently reported (2017 to early 2022) molecules as adipocyte fatty acid binding protein 4 inhibitors.

Discovery of a Novel Macrocyclic ATP Citrate Lyase Inhibitor

ATP citrate lyase (ACLY) is an important metabolic enzyme involved in the synthesis of fatty acid and cholesterol. The inhibition of ACLY is considered as a promising therapeutic strategy for various metabolic diseases and numerous malignancies. In this study, a novel macrocyclic compound 2 has been identified as a potent ACLY inhibitor with the "ring closing" strategy for conformational restriction based on NDI-091143. It showed potent ACLY inhibitory activity and binding affinity comparable to the positive control. Furthermore, compared with the positive control (T_1/2 = 3.36 min), the metabolic stability of 2 in HLMs (T_1/2 = 531.22 min) was significantly improved. All of these results characterized 2 as a promising lead compound worthy of further study.

From Data to Knowledge: Systematic Review of Tools for Automatic Analysis of Molecular Dynamics Output

An increasing number of crystal structures available on one side, and the boost of computational power available for computer-aided drug design tasks on the other, have caused that the structure-based drug design tools are intensively used in the drug development pipelines. Docking and molecular dynamics simulations, key representatives of the structure-based approaches, provide detailed information about the potential interaction of a ligand with a target receptor. However, at the same time, they require a three-dimensional structure of a protein and a relatively high amount of computational resources. Nowadays, as both docking and molecular dynamics are much more extensively used, the amount of data output from these procedures is also growing. Therefore, there are also more and more approaches that facilitate the analysis and interpretation of the results of structure-based tools. In this review, we will comprehensively summarize approaches for handling molecular dynamics simulations output. It will cover both statistical and machine-learning-based tools, as well as various forms of depiction of molecular dynamics output.

The molecular docking and molecular dynamics study of flavonol synthase and flavonoid 3'-monooxygenase enzymes involved for the enrichment of kaempferol

Kaempferol is a natural flavonol that shows many pharmacological properties including anti-inflammatory, antioxidant, anticancer, antidiabetic activities etc. It has been reported in many vegetables, fruits, herbs and medicinal plants. The enzyme flavonol synthase (FLS, EC 1.14.20.6) catalyses the conversion of dihydroflavonols to flavonols. Whereas flavonoid 3'-monooxygenase (F3'H, EC 1.14.14.82) catalyses the hydroxylation of dihydroflavonol, and flavonol. FLS is involved in the synthesis of the kaempferol whereas F3'H causes degradation of kaempferol. The present study aimed to analyse the binding affinity, stability and activating activity of enzyme FLS as well as inhibitory activity of enzyme F3'H involved in the enrichment of the kaempferol using the in-silico approaches. Computational study for physico-chemical properties, conserved domain identification, 3-D structure prediction and its validation, conservation analysis, molecular docking followed by molecular dynamics analysis of FLS and F3'H, protein-activator (FLS-LIG Complex) and protein-inhibitor (F3'H-LIG Complex) complexes have been performed. Other structural analyses like root mean square fluctuation (RMSF), root mean square deviation (RMSD), surface area solvent accessibility (SASA), radius of gyration (Rg), hydrogen bond analysis, principal component analysis (PCA), Poisson-Boltzmann analysis (MM_PBSA) and the dynamic cross correlation map (DCCM) analysis to explore the structural, functional and thermodynamic stability of the proteins and the complexes were also studied. The molecular docking result showed that FLS binds strongly with the activator ascorbate (CID _54670067) while F3'H binds with the inhibitor ketoconazole (CID_456201). The most powerful inhibitor (ketoconazole for F3'H) and activator (ascorbate for FLS) is determined by computing the thermodynamic binding free energy through MM_PBSA analysis. The current work provides wide-ranging structural and functional information about FLS and F3'H enzymes showing detailed molecular mechanism of kaempferol biosynthesis and its degradation and hence kaempferol enrichment. Finding of the present work opens up new possibilities for future research towards enrichment of kaempferol by using activator (ascorbate) for FLS and inhibitor (ketoconazole) for F3'H as well as for its large-scale production using in vitro approaches.Communicated by Ramaswamy H. Sarma.

Discovery of Ubiquitin-Specific Protease 7 (USP7) Inhibitors with Novel Scaffold Structures by Virtual Screening, Molecular Dynamics Simulation, and Biological Evaluation

USP7 has been regarded as a potential therapeutic target for cancer. In this study, virtual screening, molecular dynamics (MD) simulation, and biological evaluation have been applied for the discovery of novel USP7 inhibitors targeting the catalytic active site. Among the obtained compounds, compound 12 with a novel scaffold structure exhibited certain USP7 inhibitory activity (Ub-AMC assay IC₅₀ = 18.40 ± 1.75 μM, Ub-Rho assay IC₅₀ = 7.75 μM). The binding affinity between USP7_CD (USP7 catalytic domain) and this hit compound was confirmed with a K_D value of 4.46 ± 0.86 μM. Preliminary in vitro studies disclosed its antiproliferative activity on human prostate cancer cell line LNCaP with an IC₅₀ value of 15.43 ± 3.49 μM. MD simulation revealed the detailed differences of protein-ligand interactions between USP7_CD and the ligands, including the reference compound ALM4 and compound 12, providing some important information for improving the bioactivity of 12. This hit compound will serve as a promising starting point for facilitating the further discovery of novel USP7 inhibitors.

Computational modeling for mutational analysis of nitrilase enzyme towards enhancement of binding empathy

Nitrilase enzyme (a green catalyst) is an industrially important enzyme which hydrolyses various nitrile compounds (containing -CN functional group) into amides and corresponding carboxylic acids. The current study explored the binding affinity and a method to enhance the catalysis activity of the enzyme using computational approaches. Four mutants were generated using sequential site-directed mutagenesis aiming that an increase in hydrogen bonds that will further increase binding efficiency towards the ligand. Molecular dynamics simulation was rigorously performed to check the stability of those mutants followed by docking to verify its interaction with the ligand. Various statistical dynamics analyses were performed to validate the structure. All the studies predict that built mutants are stable. Mutants 2 and 3 showed a better affinity towards acrylamide by forming the highest number of hydrogen bonds implying better catalysis. The binding affinity values of the Mutant 2 and Mutant 3 with acrylamide are -7.44 kcal/mol and -7.17 kcal/mol, respectively. This study may prove useful for the industry to develop efficient nitrilase enzymes with improved catalytic activity.Communicated by Ramaswamy H. Sarma.

Identification of new dual FABP4/5 inhibitors based on a naphthalene-1-sulfonamide FABP4 inhibitor

Fatty acid binding protein 4 (FABP4) and fatty acid binding protein 5 (FABP5) are mainly expressed in adipocytes and/or macrophages and play essential roles in energy metabolism and inflammation. When FABP4 function is diminished, FABP5 expression is highly increased possibly as a functional compensation. Dual FABP4/5 inhibitors are expected to provide beneficial synergistic effect on treating diabetes, atherosclerosis, and inflammation-related diseases. Starting from our previously reported selective FABP4 inhibitor 8, structural biology information was used to modulate the selectivity profile and to design potent dual FABP4/5 inhibitors with good selectivity against FABP3. Two compounds A16 and B8 were identified to show inhibitory activities against both FABP4/5 and good selectivity over FABP3, which could also reduce the level of forskolin-stimulated lipolysis in mature 3T3-L1 adipocytes. Compared with compound 8, these two compounds exhibited better anti-inflammatory effects in lipopolysaccharide-stimulated RAW264.7 murine macrophages, with decreased levels of pro-inflammatory cytokines TNFα and MCP-1 and apparently inhibited IKK/NF-κB pathway.