The Pivotal Distinction between Antagonists' and Agonists' Binding into Dopamine D4 Receptor-MD and FMO/PIEDA Studies

The dopamine D4 receptor (D4R) is a promising therapeutic target in widespread diseases, and the search for novel agonists and antagonists appears to be clinically relevant. The mechanism of binding to the receptor (R) for antagonists and agonists varies. In the present study, we conducted an in-depth computational study, teasing out key similarities and differences in binding modes, complex dynamics, and binding energies for D4R agonists and antagonists. The dynamic network method was applied to investigate the communication paths between the ligand (L) and G-protein binding site (GBS) of human D4R. Finally, the fragment molecular orbitals with pair interaction energy decomposition analysis (FMO/PIEDA) scheme was used to estimate the binding energies of L-R complexes. We found that a strong salt bridge with D3.32 initiates the inhibition of the dopamine D4 receptor. This interaction also occurs in the binding of agonists, but the change in the receptor conformation to the active state starts with interaction with cysteine C3.36. Such a mechanism may arise in the case of agonists unable to form a hydrogen bond with the serine S5.46, considered, so far, to be crucial in the activation of GPCRs. The energy calculations using the FMO/PIEDA method indicate that antagonists show higher residue occupancy of the receptor binding site than agonists, suggesting they could form relatively more stable complexes. Additionally, antagonists were characterized by repulsive interactions with S5.46 distinguishing them from agonists.

Towards Polycaprolactone-Based Scaffolds for Alveolar Bone Tissue Engineering: A Biomimetic Approach in a 3D Printing Technique

The alveolar bone is a unique type of bone, and the goal of bone tissue engineering (BTE) is to develop methods to facilitate its regeneration. Currently, an emerging trend involves the fabrication of polycaprolactone (PCL)-based scaffolds using a three-dimensional (3D) printing technique to enhance an osteoconductive architecture. These scaffolds are further modified with hydroxyapatite (HA), type I collagen (CGI), or chitosan (CS) to impart high osteoinductive potential. In conjunction with cell therapy, these scaffolds may serve as an appealing alternative to bone autografts. This review discusses research gaps in the designing of 3D-printed PCL-based scaffolds from a biomimetic perspective. The article begins with a systematic analysis of biological mineralisation (biomineralisation) and ossification to optimise the scaffold's structural, mechanical, degradation, and surface properties. This scaffold-designing strategy lays the groundwork for developing a research pathway that spans fundamental principles such as molecular dynamics (MD) simulations and fabrication techniques. Ultimately, this paves the way for systematic in vitro and in vivo studies, leading to potential clinical applications.

The Significance of Halogen Bonding in Ligand-Receptor Interactions: The Lesson Learned from Molecular Dynamic Simulations of the D4 Receptor

Recently, a computational approach combining a structure-activity relationship library containing pairs of halogenated ligands and their corresponding unsubstituted ligands (called XSAR) with QM-based molecular docking and binding free energy calculations was developed and used to search for amino acids frequently targeted by halogen bonding, also known as XB hot spots. However, the analysis of ligand-receptor complexes with halogen bonds obtained by molecular docking provides a limited ability to study the role and significance of halogen bonding in biological systems. Thus, a set of molecular dynamics simulations for the dopamine D4 receptor, recently crystallized with the antipsychotic drug nemonapride (5WIU), and the five XSAR sets were performed to verify the identified hot spots for halogen bonding, in other words, primary (V5x40), and secondary (S5x43, S5x461 and H6x55). The simulations confirmed the key role of halogen bonding with V5x40 and H6x55 and supported S5x43 and S5x461. The results showed that steric restrictions and the topology of the molecular core have a crucial impact on the stabilization of the ligand-receptor complex by halogen bonding.

Incorporation of bioflavonoids from Bidens tripartite into micelles of non-ionic surfactants - experimental and theoretical studies

Classical extraction methods used for an isolation of active substances from the plant material are expensive, complicated and often environmentally unfriendly. The ultrasonic assistance micelle-mediated extraction method (UAMME) seems to be an interesting alternative. The aim of this work was to compare an efficiency of water solutions of three non-ionic surfactants: C9-11 Pareth-5, PPG-6 Steareth-7 and PPG-4 Laureth-5 in UAMME of Bidens tripartita. Subsequently, the obtained extracts were separated into two immiscible phases, a polyphenols rich surfactants phase and an aqueous phase by its heating above surfactants cloud points (CPC) or by salting out with NaCl. Along with decreasing the Hydrophilic/Lipophilic Balance (HLB) factor value of surfactants, i.e. increase of the hydrophobicity, a significant decreasing of the flavonoid content was observed. While polyphenols content and antioxidant activity increased. The good surface properties of all surfactants correspond to the high content of phenolic compounds in extracts and both concentration methods resulted in even a 50-fold increase of polyphenols content. Dynamic light scattering measurements (DLS) provided that solubilization of polyphenols, i.e. their incorporation into surfactants' micelles, occurred with significant enlarging of particle size. Based on the molecular dynamic simulations, the mechanism of polyphenols incorporation into micelles was discussed.

Formation of active species from ruthenium alkylidene catalysts-an insight from computational perspective

Ruthenium alkylidene complexes are commonly used as olefin metathesis catalysts. Initiation of the catalytic process requires formation of a 14-electron active ruthenium species via dissociation of a respective ligand. In the present work, this initiation step has been computationally studied for the Grubbs-type catalysts (H₂IMes)(PCy₃)(Cl)₂Ru=CHPh, (H₂IMes)(PCy₃)(Cl)₂Ru=CH-CH=CMe₂ and (H₂IMes)(3-Br-py)₂(Cl)₂Ru=CHPh, and the Hoveyda-Grubbs-type catalysts (H₂IMes)(Cl)₂Ru=CH(o-OiPrC₆H₄), (H₂IMes)(Cl)₂Ru=CH(5-NO₂-2-OiPrC₆H₃), and (H₂IMes)(Cl)₂Ru=CH(2-OiPr-3-PhC₆H₃), using density functional theory (DFT). Additionally, the extended-transition-state combined with the natural orbitals for the chemical valence (ETS-NOCV) and the interacting quantum atoms (IQA) energy decomposition methods were applied. The computationally determined activity order within both families of the catalysts and the activation parameters are in agreement with reported experimental data. The significance of solvent simulation and the basis set superposition error (BSSE) correction is discussed. ETS-NOCV demonstrates that the bond between the dissociating ligand and the Ru-based fragment is largely ionic followed by the charge delocalizations: σ(Ru-P) and π(Ru-P) and the secondary CH^…Cl, CH^…π, and CH^…HC interactions. In the case of transition state structures, the majority of stabilization stems from London dispersion forces exerted by the efficient CH^…Cl, CH^…π, and CH^…HC interactions. Interestingly, the height of the electronic dissociation barriers is, however, directly connected with the prevalent (unfavourable) changes in the electrostatic and orbital interaction contributions despite the favourable relief in Pauli repulsion and geometry reorganization terms during the activation process. According to the IQA results, the isopropoxy group in the Hoveyda-Grubbs-type catalysts is an efficient donor of intra-molecular interactions which are important for the activity of these catalysts.

Antifungal, anticancer, and docking studies of colchiceine complexes with monovalent metal cation salts

Complexes of colchiceine with monovalent cation perchlorates and iodides have been obtained and characterized by spectroscopic methods. DFT and spectroscopic studies reveal that the dihedral angle ω_1-1a-12-12a , crucial for colchicine biological mechanism of action, that is, binding to tubulins depends on the diameter of the complexed metal cation. Biological tests indicated no antifungal properties of colchicine (it was active only toward A.pullulans), in contrast to its derivative-(colchiceine). Complexation of colchiceine with metal cations improved significantly the antifungal potency, even below MIC <1 μg/ml. The colchiceine complexes were more potent than colchiceine, and some of them were even more potent than the fungicidal standard IPBC. The highest potency of colchiceine complexes was noted against A. pullulans (MIC = 0.5 μg/ml). In contrast to the findings concerning antifungal potency, the anticancer studies showed complexes of colchicine more active (~IC₅₀  = 2 nM) than those of colchiceine (~IC₅₀  = 6 μM). MDA-MB-231 breast cancer cell lines and human lung fibroblasts CCD39Lu were also tested.

New dual ligands for the D2 and 5-HT1A receptors from the group of 1,8-naphthyl derivatives of LCAP

More than 300 million people are suffering from depression, one of the civilization diseases in the 21st century. Serotonin 5-HT_1AR and dopamine D₂R play an important role in the treatment and pathogenesis of depression. Moreover, in recent years, the efficacy of dual 5-HT_1A/D₂ receptors ligands has been demonstrated in the fight against depression. In this work the new bulky arylpiperazine derivatives (LCAP) were synthesized in microwave radiation field. The affinities for the selected serotonin (5-HT_1A,5-HT_2A,5-HT₆,5-HT₇) and dopamine (D₂) receptors have been evaluated in vitro. Compounds 5.3a, 5.4, 5.1c, 5.3d, 5.2a are promising dual 5-HT_1AR/D₂R ligands. The SAR analysis were additionally supported with molecular docking studies.

Microwave-Assisted Synthesis of Trazodone and Its Derivatives as New 5-HT1A Ligands: Binding and Docking Studies

Trazodone, a well-known antidepressant drug widely used throughout the world, works as a 5-hydroxytryptamine (5-HT₂) and α₁-adrenergic receptor antagonist and a serotonin reuptake inhibitor. Our research aimed to develop a new method for the synthesis of trazodone and its derivatives. In the known methods of the synthesis of trazodone and its derivatives, organic and toxic solvents are used, and the synthesis time varies from several to several dozen hours. Our research shows that trazodone and its derivatives can be successfully obtained in the presence of potassium carbonate as a reaction medium in the microwave field in a few minutes. As a result of the research work, 17 derivatives of trazodone were obtained, including compounds that exhibit the characteristics of 5-HT_1A receptor ligands. Molecular modeling studies were performed to understand the differences in the activity toward 5-HT_1A and 5-HT_2A receptors between ligand 10a (2-(6-(4-(3-chlorophenyl)piperazin-1-yl)hexyl)-[1,2,4]triazolo[4,3-a]pyridin-3(2H)-one) (5-HT_1AK_i = 16 nM) and trazodone. The docking results indicate the lack of the binding of ligand 10a to 5-HT_2AR, which is consistent with the in vitro studies. On the other hand, the docking results for the 5-HT_1A receptor indicate two possible binding modes. Crystallographic studies support the hypothesis of an extended conformation.

Recognition of repulsive and attractive regions of selected serotonin receptor binding site using FMO-EDA approach

The complexes of selected long-chain arylpiperazines with homology models of 5-HT_1A, 5-HT_2A, and 5-HT₇ receptors were investigated using quantum mechanical methods. The molecular geometries of the ligand-receptor complexes were firstly optimized with the Our own N-layered Integrated molecular Orbital and molecular Mechanics (ONIOM) method. Next, the fragment molecular orbitals method with an energy decomposition analysis scheme (FMO-EDA) was employed to estimate the interaction energies in binding sites. The results clearly showed that orthosteric binding sites of studied serotonin receptors have both attractive and repulsive regions. In the case of 5-HT_1A and 5-HT_2A two repulsive areas, located in the lower part of the binding pocket, and one large area of attraction engaging many residues at the top of all helices were identified. Additionally, for the 5-HT₇ receptor, the third area of destabilization located at the extracellular end of the helix 6 was found.

Salt Bridge in Ligand-Protein Complexes-Systematic Theoretical and Statistical Investigations

Although the salt bridge is the strongest among all known noncovalent molecular interactions, no comprehensive studies have been conducted to date to examine its role and significance in drug design. Thus, a systematic study of the salt bridge in biological systems is reported herein, with a broad analysis of publicly available data from Protein Data Bank, DrugBank, ChEMBL, and GPCRdb. The results revealed the distance and angular preferences as well as privileged molecular motifs of salt bridges in ligand-receptor complexes, which could be used to design the strongest interactions. Moreover, using quantum chemical calculations at the MP2 level, the energetic, directionality, and spatial variabilities of salt bridges were investigated using simple model systems mimicking salt bridges in a biological environment. Additionally, natural orbitals for chemical valence (NOCV) combined with the extended-transition-state (ETS) bond-energy decomposition method (ETS-NOCV) were analyzed and indicated a strong covalent contribution to the salt bridge interaction. The present results could be useful for implementation in rational drug design protocols.

Pyrroloquinoline scaffold-based 5-HT6R ligands: Synthesis, quantum chemical and molecular dynamic studies, and influence of nitrogen atom position in the scaffold on affinity

Based on pyrroloquinoline scaffold bearing 5-HT_2C agonists, a series of arylsulfonamide derivatives of 1H-pyrrolo[2,3-f]quinoline and 1H-pyrrolo[3,2-h]quinoline, substituted at position 3 with tetrahydropyridine, were synthesized and evaluated in vitro for their affinity for 5-HT₆ receptors. A structure-activity relationship study showed that the 1H-pyrrolo[3,2-h]quinoline scaffold was more favorable for 5-HT₆R binding than the 1H-pyrrolo[2,3-f]quinoline one, suggesting dependence upon the type of condensation of the pyrrole and quinoline rings. As revealed by quantum-chemical calculations and molecular dynamic studies, position of the quinoline nitrogen atom in the planar pyrroloquinoline skeleton might affect the spatial orientation of the arylsulfonyl fragment, as a result of structure stabilization by internal hydrogen bonds.

The Effect of Carboxamide/Sulfonamide Replacement in Arylpiperazinylalkyl Derivatives on Activity to Serotonin and Dopamine Receptors

A series of carboxamide and sulfonamide alkyl (p-xylyl and benzyl) 1-(2-methoxyphenyl)piperazine (o-OMe-PhP) and 1-(2,3-dichlorophenyl)piperazine (2,3-DCPP) analogs were prepared and tested for their affinity to bind to serotonin 5-HT_1A /5-HT₆ /5-HT₇ and dopamine D₂ receptors. This chemical modification let us explore the impact of the replacement of the carboxamide by the sulfonamide group on the affinity changes. In both the o-OMe-PhP and 2,3-DCPP series, the relative activities of the carboxamides versus sulfonamides toward the 5-HT_1A /5-HT₆ /5-HT₇ and D₂ receptors show similar trends. Varied or similar activities for particular receptors were found for the carboxamides/sulfonamides with p-xylyl spacer, while of the two classes of carboxamides and sulfonamides examined, benzyl derivatives of the sulfonamides displayed the highest serotoninergic affinity, in particular to the 5-HT₇ receptors (K_i 8-85 nM). The K_i values revealed that, irrespective of the carboxamide/sulfonamide zone, both p-xylyl and benzyl derivatives had the highest affinity for the dopamine D₂ receptor (i.e., 16 out of 24 compounds investigated have an affinity below 100 nM). A molecular modeling study of carboxamide 9a and sulfonamide 9b showed that their binding effects to each of 5-HT_1A R and D₂ R created binding modes interaction with different conserved receptors residues. Structural similarities of carboxamide 9a in complexes with a 5-HT_1A R (9aI) and D₂ R (9aII) are over 83%, while the respective similarities of sulfonamide 9b structures (9bI/9bII) are only about 40%.