Types Of Ligands Research Articles

Quantitative and functional characterisation of extracellular vesicles after passive loading with hydrophobic or cholesterol-tagged small molecules

Extracellular vesicles (EVs) are nanosized intercellular messengers that bear enormous application potential as biological drug delivery vehicles. Much progress has been made for loading or decorating EVs with proteins, peptides or RNAs using genetically engineered donor cells, but post-isolation loading with synthetic drugs and using EVs from natural sources remains challenging. In particular, quantitative and unambiguous data assessing whether and how small molecules associate with EVs versus other components in the samples are still lacking. Here we describe the systematic and quantitative characterisation of passive EV loading with small molecules based on hydrophobic interactions - either through direct adsorption of hydrophobic compounds, or by membrane anchoring of hydrophilic ligands via cholesterol tags. As revealed by single vesicle imaging, both ligand types bind to CD63 positive EVs (exosomes), however also non-specifically to other vesicles, particles, and serum proteins. The hydrophobic compounds Curcumin and Terbinafine aggregate on EVs with no apparent saturation up to 106–107 molecules per vesicle as quantified by liquid chromatography – high resolution mass spectrometry (LC-HRMS). For both compounds, high density EV loading resulted in the formation of a population of large, electron-dense vesicles as detected by quantitative cryo-transmission electron microscopy (TEM), a reduced EV cell uptake and a toxic gain of function for Curcumin-EVs. In contrast, cholesterol tagging of a hydrophilic mdm2-targeted cyclic peptide saturated at densities of ca 104–105 molecules per vesicle, with lipidomics showing addition to, rather than replacement of endogenous cholesterol. Cholesterol anchored ligands did not change the EVs' size or morphology, and such EVs retained their cell uptake activity without inducing cell toxicity. However, the cholesterol-anchored ligands were rapidly shed from the vesicles in presence of serum. Based on these data, we conclude that (1) both methods allow loading of EVs with small molecules but are prone to unspecific compound binding or redistribution to other components if present in the sample, (2) cholesterol anchoring needs substantial optimization of formulation stability for in vivo applications, whereas (3) careful titration of loading densities is warranted when relying on hydrophobic interactions of EVs with hydrophobic compounds to mitigate changes in physicochemical properties, loss of EV function and potential cell toxicity.

Tunable Fluorescence from 2D Assemblies of LnW10 and P2W18 Polyoxometalates Clusters with Quaternary Ammonium‐type AIEgens

AbstractTwo‐dimensional (2D) AIE‐inorganic nanocomposites exhibit high stability and high fluorescence activity. However, limited by the types and properties of 2D inorganic materials, it's challenging to realize complex structures and functions. We designed a quaternary ammonium‐type AIE ligand, TPECholine. We chose TPECholine and POM clusters as building blocks and synthesized a series of single‐layer nanosheets (SLNSs) by assembling LnW10 or P2W18 POM clusters with TPECholine. By regulating the types of POM clusters and ligands, the morphology and fluorescence intensity of the SLNSs can be finely tuned. Due to the restriction of the intramolecular motions of AIEgens by the SLNSs, nanosheets can exhibit promoted quantum yield (up to 76 %). In addition, thanks to the sub‐nanometric sizes and excess surface charges, SLNSs exhibit excellent solvent compatibility, including water, chloroform, ethanol, etc. And the nanosheets showed high fluorescence intensity in these solvents.

Tunable Fluorescence from 2D Assemblies of LnW10 and P2W18 Polyoxometalates Clusters with Quaternary Ammonium-type AIEgens.

Two-dimensional (2D) AIE-inorganic nanocomposites exhibit high stability and high fluorescence activity. However, limited by the types and properties of 2D inorganic materials, it's challenging to realize complex structures and functions. We designed a quaternary ammonium-type AIE ligand, TPECholine. We chose TPECholine and POM clusters as building blocks and synthesized a series of single-layer nanosheets (SLNSs) by assembling LnW10 or P2W18 POM clusters with TPECholine. By regulating the types of POM clusters and ligands, the morphology and fluorescence intensity of the SLNSs can be finely tuned. Due to the restriction of the intramolecular motions of AIEgens by the SLNSs, nanosheets can exhibit promoted quantum yield (up to 76%). In addition, thanks to the sub-nanometric sizes and excess surface charges, SLNSs exhibit excellent solvent compatibility, including water, chloroform, ethanol, etc. And the nanosheets showed high fluorescence intensity in these solvents.

Synthesis of Aluminum-Based Metal-Organic Framework (MOF)-Derived Carbon Nanomaterials and Their Water Adsorption Isotherm.

The characteristics of water vapor adsorption depend on the structure, porosity, and functional groups of the material. Metal-organic framework (MOF)-derived carbon (MDC) is a novel material that exhibits a high specific area and tunable pore sizes by exploiting the stable structure and porosity of pure MOF materials. Herein, two types of aluminum-based MOFs were used as precursors to synthesize hydrophobic microporous C-MDC and micro-mesoporous A-MDC via carbonization and activation depending on the type of ligands in the precursors. C-MDC and A-MDC have different pore characteristics and exhibit distinct water adsorption properties. C-MDC with hydrophobic properties and micropores exhibited negligible water adsorption (108.54 mgg-1) at relatively low pressures (P/P0~0.3) but showed a rapid increase in water adsorption ability (475.7 mgg-1) at relative pressures of about 0.6. A comparison with the isotherm model indicated that the results were consistent with the theories, which include site filling at low relative pressure and pore filling at high relative pressure. In particular, the Do-Do model specialized for type 5 showed excellent agreement.

Diaryl(fluorinated)-mercury species as potential precursors of triaryl(fluorinated)-gallium to be used in the synthesis of cyclometallated Ga compounds and unexpected formation of aryl-Ga clusters

The first goal of this work was to explore the feasibility of diaryl-mercury species as the synthetic precursors of triaryl-gallium species GaAr*3 (where Ar*= pH, 4; Ar*= 3,5-difluorophenyl, 5; and Ar*= 3,5-trifluoromethylphenyl, 6). Expecting that 4–6 behave as Lewis acids of different strength, the second purpose was to use them for the synthesis of either rollover or classic cyclometallated Ga compounds. Three analogous diaryl-mercury HgAr*2 species, 1–3, were successfully synthesized. The structures of compounds 2 and 3 were confirmed by gas chromatography - mass spectrometry experiments. Additionally, compound 3 was analyzed through X-ray diffraction; in the crystal structure obtained, π-stacking interactions were observed. The only Ga compound synthesized was GaPh3, 4, because the presence of fluorine-containing groups in meta-position caused sublimation of the respective mercury diaryl compounds, impeding their reaction with gallium. The attempts toward the synthesis of the rollover or classic cyclometallated compounds in the reaction of 4 with bipyridine-, pyrazole- or benzo-imidazole- type ligands have failed. On the other hand, under the experimental conditions applied, water traces favored formation of the solid aryl-Ga cluster containing twelve Ga atoms [Ga12], whereas the above-mentioned ligands were quantitatively recovered in the solution. The identity of aryl-gallium cluster was confirmed by electrospray ionization - high resolution mass spectrometry. Although Ga cluster was not expected, it is considered an important finding of this work, owing to the variety of possible applications and still limited data available on the synthesis and structural characterization of such compounds.

Tetrahedral Imidazolate Frameworks with Auxiliary Ligands (TIF-Ax): Synthetic Strategies and Applications.

Zeolitic imidazolate frameworks (ZIFs) are an important subclass of metal-organic frameworks (MOFs). Recently, we reported a new kind of MOF, namely tetrahedral imidazolate frameworks with auxiliary ligands (TIF-Ax), by adding linear ligands (Hint) into the zinc-imidazolate system. Introducing linear ligands into the M2+-imidazolate system overcomes the limitation of imidazole derivatives. Thanks to the synergistic effect of two different types of ligands, a series of new TIF-Ax with interesting topologies and a special pore environment has been reported, and they have attracted extensive attention in gas adsorption, separation, catalysis, heavy metal ion capture, and so on. In this review, we give a comprehensive overview of TIF-Ax, including their synthesis methods, structural diversity, and multi-field applications. Finally, we also discuss the challenges and perspectives of the rational design and syntheses of new TIF-Ax from the aspects of their composition, solvent, and template. This review provides deep insight into TIF-Ax and a reference for scholars with backgrounds of porous materials, gas separation, and catalysis.

Chemical and structural changes of resins during the catalytic and non-catalytic aquathermolysis of heavy crude oils

Resins are important molecules for colloidal system (maintaining asphaltenes dispersed) of heavy oils and are responsible of their high viscosity (together with asphaltenes). The results of characterization of resins before and after aquathermolysis by molecular weight, elemental analysis, Fourier transform infrared, nuclear magnetic resonance, and ultraviolet fluorescence were collected and analyzed to highlight the changes in chemical and structural properties. The discussion is based on the transformations that resin molecules undergo via hydrogenation, deoxygenation, desulfurization, cracking, ring opening, dealkylation and pyrolysis reactions at steam injection conditions. Some correlations were developed between properties of resins. It was found that the type of ligand plays an important role for catalytic aquathermolysis besides the type of active metal since a synergic effect of these factors produces diverse results in the properties of resins. The molecular weight of resins is greater improved using oil-soluble catalysts compared with water-soluble catalysts and non-catalytic aquathermolysis. Mo-based catalysts usually exhibit higher hydrogenation capability and sulfur removal than other active metals, while Fe-based catalysts commonly improves dealkylation and pyrolysis of side chain reactions of resins.

Design of Tracers in Fluorescence Polarization Assay for Extensive Application in Small Molecule Drug Discovery.

Development of fluorescence polarization (FP) assays, especially in a competitive manner, is a potent and mature tool for measuring the binding affinities of small molecules. This approach is suitable for high-throughput screening (HTS) for initial ligands and is also applicable for further study of the structure-activity relationships (SARs) of candidate compounds for drug discovery. Buffer and tracer, especially rational design of the tracer, play a vital role in an FP assay system. In this perspective, we provided different kinds of approaches for tracer design based on successful cases in recent years. We classified these tracers by different types of ligands in tracers, including peptide, nucleic acid, natural product, and small molecule. To make this technology accessible for more targets, we briefly described the basic theory and workflow, followed by highlighting the design and application of typical FP tracers from a perspective of medicinal chemistry.

Unlocking the Potential of Colloidal Quantum Dot/Organic Hybrid Solar Cells: Band Tunable Interfacial Layer Approach.

Hybrid colloidal quantum dot (CQD)/organic architectures are promising candidates for emerging optoelectronic devices having high performance and inexpensive fabrication. For unlocking the potential of CQD/organic hybrid devices, enhancing charge extraction properties at electron transport layer (ETL)/CQD interfaces is crucial. Hence, we carefully adjust the interface properties between the ETL and CQD layer by incorporating an interfacial layer for the ETL (EIL) using several types of cinnamic acid ligands. The EIL having a cascading band offset (ΔEC) between the ETL and CQD layer suppresses the potential barrier and the local charge accumulation at ETL/CQD interfaces, thereby reducing the bimolecular recombination. An optimal EIL effectively expands the depletion region that facilitates charge extraction between the ETL and CQD layer while preventing the formation of shallow traps. Representative devices with an EIL exhibit a maximum power conversion efficiency of 14.01% and retain over 80% of initial performances after 300 h under continuous maximum power point operation.

An electrochemical study of the dissolution behavior of gold in a novel glycine-thiosulfate system

Ammonia-free thiosulfate systems are known for their non-toxicity, low reagent consumption, and excellent leaching efficiency in gold extraction studies. This study proposes a novel and environmentally friendly glycine-thiosulfate system and comprehensively investigates the dissolution behavior of gold through the application of electrochemical methods. Electrochemical quartz crystal microbalance (EQCM) has demonstrated that the anodic dissolution of gold is predominantly influenced by the forms of copper(II)-glycine complexes as catalysts, and the presence of Cu(C2H4NO2)3− complex in strong alkaline has enhanced dissolution rate of gold, in contrast to Cu(C2H4NO2)20 complex in near-nurture condition. Such excellent catalytic capability of the Cu(C2H4NO2)3− complex for gold dissolution can be attributed to the lowest corrosion potential, slighter passivation behavior, and rapid electron transfer from the analysis of corrosion electrochemistry (OCP, PDP, and EIS) and advanced spectrum technologies (LA-ICP-MS and XPS). The dissolution of gold in the novel glycine-thiosulfate system undergoes a typical ligand exchange process (Au+→Au(C2H4NO2)2−→Au(S2O3)23−), and the formation of passivation species on the gold surface is predominantly formed by Au(I)-glycine coordination, rather than the sulfur-containing products from thiosulfate decomposition. Based on these results, the proposed two electrochemical reaction mechanisms will contribute to the optimization of leaching conditions in the novel glycine-thiosulfate system.

T-cell immunoglobulin and mucin-domain containing-3 (TIM-3): Solving a key puzzle in autoimmune diseases.

Dysfunctional immune cells participate in the pathogenesis of a variety of autoimmune diseases, although the specific mechanisms remain elusive and effective clinical interventions are lacking. Recent research on immune checkpoint molecules has revealed significant expression of T cell immunoglobulin and mucin domain-containing protein 3 (TIM-3) on the surfaces of various immune cells. These include different subsets of T cells, macrophages, dendritic cells, natural killer cells, and mast cells. Further investigation into its protein structure, ligands, and intracellular signaling pathway activation mechanisms has found that TIM-3, by binding with different ligands, is involved in the regulation of crucial biological processes such as proliferation, apoptosis, phenotypic transformation, effector protein synthesis, and cellular interactions of various immune cells. The TIM-3-ligand axis plays a pivotal role in the pathogenesis of numerous conditions, including autoimmune diseases, infections, cancers, transplant rejection, and chronic inflammation. This article primarily focuses on the research findings of TIM-3 in the field of autoimmune diseases, with a special emphasis on the structure and signaling pathways of TIM-3, its types of ligands, and the potential mechanisms implicated in systemic lupus erythematosus, multiple sclerosis, rheumatoid arthritis, as well as other autoimmune diseases and chronic inflammation. The latest research results in the field of immunology suggest that TIM-3 dysfunction affects various immune cells and participates in the pathogenesis of diseases. Monitoring the activity of its receptor-ligand axis can serve as a novel biological marker for disease clinical diagnosis and prognosis evaluation. More importantly, the TIM-3-ligand axis and the downstream signaling pathway molecules may become key targets for targeted intervention treatment of autoimmune-related diseases.

A Chemist's View on Electronic and Steric Effects of Surface Ligands on Plasmonic Metal Nanostructures.

ConspectusPlasmonic metal nanostructures have been extensively developed over the past few decades because of their ability to confine light within the surfaces and manipulate strong light-matter interactions. The light energy stored by plasmonic nanomaterials in the form of surface plasmons can be utilized to initiate chemical reactions, so-called plasmon-induced catalysis, which stresses the importance of understanding the surface chemistry of the plasmonic materials. Nevertheless, only physical interpretation of plasmonic behaviors has been a dominant theme, largely excluding chemical intuitions that facilitate understanding of plasmonic systems from molecular perspectives. To overcome and address the lack of this complementary understanding based on molecular viewpoints, in this Account we provide a new concept encompassing the well-developed physics of plasmonics and the corresponding surface chemistry while reviewing and discussing related references. Inspired by Roald Hoffmann's descriptions of solid-state surfaces based on the molecular orbital picture, we treat molecular interfaces of plasmonic metal nanostructures as a series of metal-ligand complexes. Accordingly, the effects of the surface ligands can be described by bisecting them into electronic and steric contributions to the systems. By exploration of the quality of orbital overlaps and the symmetry of the plasmonic systems, electronic effects of surface ligands on localized surface plasmon resonances (LSPRs), surface diffusion rates, and hot-carrier transfer mechanisms are investigated. Specifically, the propensity of ligands to donate electrons in a σ-bonding manner can change the LSPR by shifting the density of states near the Fermi level, whereas other types of ligands donating or accepting electrons in a π-bonding manner modulate surface diffusion rates by affecting the metal-metal bond strength. In addition, the formation of metal-ligand bonds facilitates direct hot-carrier transfer by forming a sort of molecular orbital between a plasmonic structure and ligands. Furthermore, effects of steric environments are discussed in terms of ligand-ligand and ligand-surface nonbonding interactions. The steric hindrance allows for controlling the accessibility of the surrounding chemical species toward the metal surface by modulating the packing density of ligands and generating repulsive interactions with the surface atoms. This unconventional approach of considering the plasmonic system as a delocalized molecular entity could establish a basis for integrating chemical intuition with physical phenomena. Our chemist's outlook on a molecular interface of the plasmonic surface can provide insights and avenues for the design and development of more exquisite plasmonic catalysts with regio- and enantioselectivities as well as advanced sensors with unprecedented chemical controllability and specificity.

VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical Simulations.

Modeling and simulation of small molecules such as drugs and biological cofactors have been both a major focus of computational chemistry for decades and a growing need among computational biophysicists who seek to investigate the interaction of different types of ligands with biomolecules. Of particular interest in this regard are quantum mechanical (QM) calculations that are used to more accurately describe such small molecules, which can be of heterogeneous structures and chemistry, either in purely QM calculations or in hybrid QM/molecular mechanics (MM) simulations. QM programs are also used to develop MM force field parameters for small molecules to be used along with established force fields for biomolecules in classical simulations. With this growing need in mind, here we report a set of software tools developed and closely integrated within the broadly used molecular visualization/analysis program, VMD, that allow the user to construct, modify, and parametrize small molecules and prepare them for QM, hybrid QM/MM, or classical simulations. The tools also provide interactive analysis and visualization capabilities in an easy-to-use and integrated environment. In this paper, we briefly report on these tools and their major features and capabilities, along with examples of how they can facilitate molecular research in computational biophysics that might be otherwise prohibitively complex.

Chiral PSiSi-Ligand Enabled Iridium-Catalyzed Atroposelective Intermolecular C-H Silylation.

Catalytic enantioselective intermolecular C-H silylation offers an efficient approach for the rapid construction of chiral organosilicon compounds, but remains a significant challenge. Herein, a new type of chiral silyl ligand is developed, which enables the first iridium-catalyzed atroposelective intermolecular C-H silylation reaction of 2-arylisoquinolines. This protocol features mild reaction conditions, high atom economy, and remarkable yield with excellent stereoselectivity (up to 99% yield, 99% ee), delivering enantioenriched axially chiral silane platform molecules with facile convertibility. Key to the success of this unprecedented transformation relies on a novel chiral PSiSi-ligand, which facilitates the intermolecular C-H silylation process with perfect chem-, regio- and stereo-control via a multi-coordinated silyl iridium complex.

Chiral PSiSi‐Ligand Enabled Iridium‐Catalyzed Atroposelective Intermolecular C−H Silylation

AbstractCatalytic enantioselective intermolecular C−H silylation offers an efficient approach for the rapid construction of chiral organosilicon compounds, but remains a significant challenge. Herein, a new type of chiral silyl ligand is developed, which enables the first iridium‐catalyzed atroposelective intermolecular C−H silylation reaction of 2‐arylisoquinolines. This protocol features mild reaction conditions, high atom economy, and remarkable yield with excellent stereoselectivity (up to 99 % yield, 99 % ee), delivering enantioenriched axially chiral silane platform molecules with facile convertibility. Key to the success of this unprecedented transformation relies on a novel chiral PSiSi‐ligand, which facilitates the intermolecular C−H silylation process with perfect chem‐, regio‐ and stereo‐control via a multi‐coordinated silyl iridium complex.

Base Metal Catalyst for Indirect Hydrogenation of CO2.

We herein report a novel Mn-SNS-based catalyst, which is capable of performing indirect hydrogenation of CO2 to methanol via formylation. In this domain of CO2 hydrogenation, pincer ligands have shown a clear predominance. Our catalyst is based on the SNS-type tridentate ligand, which is quite stable and cheap as compared to the pincer type ligands. The catalyst can also be recycled effectively after the formylation reaction without any significant change in efficiency. Various amines including both primary and secondary amines worked well under the protocol to provide the desired formylated product in good yields. The formed formylated amines can also be reduced further at higher pressures of hydrogen. As a whole, we have developed a protocol that involves indirect CO2 hydrogenation to methanol that proceeds via formylation of amines.

Controlled spatial characteristics of ligands on nanoparticles: Determinant of cellular functions

Interactions of various ligands and receptors have been extensively investigated because they regulate a series of signal transduction leading to various functional cellular outcomes. The receptors on cell membrane recognize their specific ligands, resulting in specific binding between ligands and receptors. Accumulating evidence reveals that the receptors recognize the difference on the spatial characteristics of ligands as well as the types of ligands. Thus, control on spatial characteristics of multiple ligands presented on therapeutic nanoparticles is believed to impact the cellular functions. Specifically, the localized and multivalent distribution of ligands on nanoparticles can induce receptor oligomerization and receptor clustering, controlling intensity or direction of signal transduction cascades. Here, we will introduce recent studies on the use of material-based nanotechnology to control spatial characteristics of ligands and their effect on cellular functions. These therapeutic nanoparticles with controlled spatial characteristics of ligands may be a promising strategy for maximized therapeutic outcome.

Activation of transient receptor potential channels is involved in reactive oxygen species (ROS)-dependent regulation of blood flow by (-)-epicatechin tetramer cinnamtannin A2

Intervention trials confirmed that blood flow-mediated dilatation increases significantly after intake of astringent (-)-epicatechin (EC) oligomers (procyanidins)-rich foods, but the mechanism remains unclear. We have previously found that procyanidins can activate the sympathetic nervous and subsequently increase blood flow. Here, we examined whether procyanidin-derived reactive oxygen species (ROS) activate transient receptor potential (TRP) channels in gastrointestinal sensory nerves and consequently induce sympathoexcitation. We evaluated the redox properties of EC and its tetramer cinntamtannin A2 (A2) at pH 5 or 7, mimicking plant vacuole or oral cavity/small intestine using a luminescent probe. At pH 5, A2 or EC showed O2·- scavenging ability, but they promoted O2·- generation at pH 7. We observed blood flow in rat cremaster arterioles using laser Doppler, a single oral dose of 10 µg/kg A2 markedly increased blood flow, while EC showed little activity. This change with A2 was significantly dampened by co-administration of adrenaline blocker, ROS scavenger N-acetyl-L-cysteine (NAC), TRP vanilloid 1, or ankyrin 1 antagonist. We also performed a docking simulation of EC or A2 with the binding site of a typical ligand for each TRP channel and calculated the respective binding affinities. The binding energies were notably higher for A2 than typical ligands, suggesting that A2 is less likely to bind to these sites. ROS produced at neutral pH following the orally administered A2 to the gastrointestinal tract could activate TRP channels, triggering sympathetic hyperactivation and causing hemodynamic changes.

Characterizing RNA-binding ligands on structures, chemical information, binding affinity and drug-likeness

ABSTRACT Recent studies suggest RNAs act as promising drug targets. However, limited development has been achieved in detecting RNA–ligand interactions. To guide the discovery of RNA-binding ligands, it is necessary to characterize them comprehensively, especially in the binding specificity, binding affinity and drug-like properties. We established a database, RNALID (http://biomed.nscc-gz.cn/RNALID/html/index.html#/database), which collects RNA–ligand interactions validated by low-throughput experiment. RNALID contains 358 RNA–ligand interactions. Comparing to the fellow database, 94.5% of ligands in RNALID are completely or partially novel collections, and 51.78% have novel two-dimensional (2D) structures. Through the analysis of ligand structure, binding affinity and cheminformatic parameters we found that multivalent (MV) ligands mainly binding to RNA repeats are more structurally conserved in both 2D and 3D structures than other ligand types, exhibit higher binding specificity and binding affinity than ligands binding to non-repeat RNAs, but deviate far from the Lipinski’s rule of five. In contrary, small molecule (SM) ligands binding to virus RNA exhibit higher affinity and more resemble protein-ligands, but potentially possess low binding specificity. Further analysis on 28 detailed drug-likeness properties indicated that RNA-ligands’ development need to balance between the binding affinity and the drug-likeness because of the significant linear co-relationship between the two. Comparing RNALID ligands to FDA-approved drugs and ligands without bioactivity indicated that RNA-binding ligands are different from them in chemical properties, structural properties and drug-likeness. Thus, characterizing the RNA–ligand interactions in RNALID in multiple respects provides new insights into discovering and designing druggable ligands binding with RNA.

Interactions of coumarin and amine ligands with six cytochrome P450 2D6 allelic variants: Molecular docking

Human CYP2D6 contributes extensively to the biotransformation of important therapeutic drugs. CYP2D6 substrate and inhibitor specificity may be affected by genetic polymorphism. This study aimed to characterize interactions of three typical ligands, 3-cyano-7-ethoxycoumarin, fluoxetine and terbinafine with six CYP2D6 variants using molecular docking simulations. The compounds were docked individually to the CYP2D6 models based on published crystal structure (PDB code: 3TBG). All ligands bound within the active site pocket near the heme. Binding involved residues found in critical secondary structures that formed the active site boundary: B-C loop, F helix, F-G loop, β-1 strands and I helix. Twenty-five amino acids were involved in the binding, and all were located in the known substrate recognition sites. Hydrophobic bonds involving phenylalanine (Phe120, Phe384) dominated CEC binding whereas electrostatic bonds between the protonated nitrogen with acidic residues (Glu216, Glu222, Asp301) dominated in binding of fluoxetine and terbinafine. Collectively, the subtle structural changes in the active site and substrate access channels induced by the mutations in the variants contributed to differential ligand docking poses. This study has provided insights into important molecular properties for CYP2D6 catalysis and inhibition, and formed basis for further exploration of structural determinants for potency and specificity of CYP2D6 ligands.