X-ray Crystallography Research Articles

Octahedral Oxo-Bridged Tri-Nickel(II) Complex with 1,3,5-Tris(2-hydroxyphenyl)-2,4-diazapenta-1,3-diene

An octahedral nickel(II) complex of 1,3,5-tris(2-hydroxyphenyl)-2,4-diazapenta-1,3-diene was obtained and characterized by X-ray crystallography. The organic ligand was obtained by the reaction of 2-hydroxybenzaldehyde with aqueous ammonia solution.

A general strategy for engineering GU base pairs to facilitate RNA crystallization.

X-ray crystallography is a fundamental technique that provides atomic-level insights into RNA structures. However, obtaining crystals of RNA structures diffracting to high resolution is challenging. We introduce a simple strategy to enhance the resolution limit of RNA crystals by the selective substitution of Watson-Crick pairs by GU pairs within RNA sequences. Our approach has successfully yielded high-resolution structures for eight unique RNA crystals. Notably, six instances showed marked resolution enhancement upon GC/AU to GU base pair substitution, with two cases achieving high-resolution structures from initially poor data. In one case, reverting GU to GC base pairs also improved resolution. Our method facilitated the first structural determinations of the Long Interspersed Nuclear Element-1 and Olfactory Receptor family 4 subfamily K member 15 ribozymes, the 2'-deoxyguanosine-III riboswitch and the Broccoli RNA aptamer. The placement of GU base pairs within the first 5' helical stem of any given RNA species, or in one peripheral stem, is shown to be sufficient. These results offer a simple and effective approach for designing sequences or selecting sequences from homologous sequences, for high-resolution RNA structure determination.

Ligand identification in CryoEM and X-ray maps using deep learning.

Accurately identifying ligands plays a crucial role in the process of structure-guided drug design. Based on density maps from X-ray diffraction or cryogenic-sample electron microscopy (cryoEM), scientists verify whether small-molecule ligands bind to active sites of interest. However, the interpretation of density maps is challenging, and cognitive bias can sometimes mislead investigators into modeling fictitious compounds. Ligand identification can be aided by automatic methods, but existing approaches are available only for X-ray diffraction and are based on iterative fitting or feature-engineered machine learning rather than end-to-end deep learning. Here, we propose to identify ligands using a deep-learning approach that treats density maps as 3D point clouds. We show that the proposed model is on par with existing machine learning methods for X-ray crystallography while also being applicable to cryoEM density maps. Our study demonstrates that electron density map fragments can aid the training of models that can later be applied to cryoEM structures but also highlights challenges associated with the standardization of electron microscopy maps and the quality assessment of cryoEM ligands. Code and model weights are available on GitHub at https://github.com/jkarolczak/ligands-classification. An accompanying ChimeraX bundle is available at https://github.com/wtaisner/chimerax-ligand-recognizer.

Similar but Distinct-Biochemical Characterization of theStaphylococcus aureus Serine Hydrolases FphHand FphI.

Staphylococcus aureus is a major cause of infections like bacteremia, pneumonia, and endocarditis. These infections are often linked to the ability of S. aureus to form biofilms. Several S. aureus serine hydrolases have previously been identified to be active during biofilm-forming conditions. Here, we present the biochemical characterization of two of these enzymes-fluorophosphonate binding hydrolase H and I (FphH, FphI). Cryogenic and room-temperature X-ray crystallography, enzymatic substrate profiling, small-angle X-ray scattering analysis, and molecular dynamics simulations provide new insights into similarities and differences between these two hydrolase_4 domain family members. We discover that these enzymes share an overall fold, including a flexible lid or cap region above the active site, which can be seen to be mobile in solution. Differences in the active site pocket and lid residues differentiate them and explain speed differences in their carboxyesterase substrate profile toward small unbranched carbon chain ester molecules. The first analysis of FphI is also compared to our previous knowledge of FphH and its association to stress conditions. These results enable the future precise targeting of Fph serine hydrolase family members with a long-term goal to significantly improve the health and wellbeing of individuals and populations worldwide.

Designing of new trans-stilbene derivative: An entry barrier of Zika virus in host cell.

A large population in the world lives in tropical and subtropical regions, showing a high risk of Zika viral infection which leads to a situation of global health emergency and demands extensive research to create effective antiviral medicines. Herein, we introduce the design of a new derivatized trans-stilbene molecule to investigate the inhibition of Zika virus entry into the host cell by molecular docking approach. The synthesized compound has been characterized by different analytical techniques such as FTIR, 1H NMR,13C NMR and UV-visible spectroscopy as well as Mass spectrometry (MS). Moreover, the complete structure elucidation was achieved via X-ray crystallography and DFT analysis. The article describes the life cycle and genome of the Zika virus along with its mechanism of entry inhibition by illustrating the structure and function of the ZIKV envelop (E) protein. The docking studies disclosed that the newly synthesized stilbene compound confers an excellent inhibitory response towards the entry of Zika virus in host cells as supported by calculated docking score and its binding conformation with Zika virus E-protein. Further, the normal mode analysis (NMA) simulation technique is used to predict the conformational states of the target E-protein, which explains the potency of the compound to bind with the Zika virus E-protein. We hope that the present study will help and encourage researchers in the field of medicinal chemistry to develop potential drugs against the Zika virus.

Natural Product Identification and Molecular Docking Studies of Leishmania Major Pteridine Reductase Inhibitors.

Background/Objectives: Pteridine reductase 1 (PTR1) has been one of the prime targets for discovering novel antileishmanial therapeutics in the fight against Leishmaniasis. This enzyme catalyzes the NADPH-dependent reduction of pterins to their tetrahydro forms. While chemotherapy remains the primary treatment, its effectiveness is constrained by drug resistance, unfavorable side effects, and substantial associated costs. Methods: This study addresses the urgent need for novel, cost-effective drugs by employing in silico techniques to identify potential lead compounds targeting the PTR1 enzyme. A library of 1463 natural compounds from AfroDb and NANPDB, prefiltered based on Lipinski's rules, was used to screen against the LmPTR1 target. The X-ray structure of LmPTR1 complexed with NADP and dihydrobiopterin (Protein Data Bank ID: 1E92) was identified to contain the critical residues Arg17, Leu18, Ser111, Phe113, Pro224, Gly225, Ser227, Leu229, and Val230 including the triad of residues Asp181-Tyr194-Lys198, which are critical for the catalytic process involving the reduction of dihydrofolate to tetrahydrofolate. Results: The docking yielded 155 compounds meeting the stringent criteria of -8.9 kcal/mol instead of the widely used -7.0 kcal/mol. These compounds demonstrated binding affinities comparable to the known inhibitors; methotrexate (-9.5 kcal/mol), jatrorrhizine (-9.0 kcal/mol), pyrimethamine (-7.3 kcal/mol), hardwickiic acid (-8.1 kcal/mol), and columbamine (-8.6 kcal/mol). Protein-ligand interactions and molecular dynamics (MD) simulation revealed favorable hydrophobic and hydrogen bonding with critical residues, such as Lys198, Arg17, Ser111, Tyr194, Asp181, and Gly225. Crucial to the drug development, the compounds were physiochemically and pharmacologically profiled, narrowing the selection to eight compounds, excluding those with potential toxicities. The five selected compounds ZINC000095486253, ZINC000095486221, ZINC000095486249, 8alpha-hydroxy-13-epi-pimar-16-en-6,18-olide, and pachycladin D were predicted to be antiprotozoal (Leishmania) with Pa values of 0.642, 0.297, 0.543, 0.431, and 0.350, respectively. Conclusions: This study identified five lead compounds that showed substantial binding affinity against LmPTR1 as well as critical residue interactions. A 100 ns MD combined with molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) calculations confirmed the robust binding interactions and provided insights into the dynamics and stability of the protein-ligand complexes.

DNA Mimic Foldamer Recognition of a Chromosomal Protein.

Helical aromatic oligoamide foldamers bearing anionic side chains that mimic the overall shape and charge surface distribution of DNA were synthesized. Their interactions with chromosomal protein Sac7d, a non-sequence-selective DNA-binder that kinks DNA, were investigated by Surface Plasmon Resonance (SPR), Isothermal Titration Calorimetry (ITC), Circular Dichroism spectroscopy (CD), melting curve analysis, Atomic Force Microscopy (AFM), and Nuclear Magnetic Resonance (NMR), as well as by single crystal X-ray crystallography. The foldamers were shown to bind to Sac7d better than a DNA duplex of comparable length. The interaction is diastereoselective and takes place at the DNA binding site. Crystallography revealed that the DNA mimic foldamers have a binding mode of their own and that they can bind to Sac7d without being kinked.

Synthesis, Crystallographic Structure, Stability, and HSA-Binding Affinity of a Novel Copper(II) Complex with Pyridoxal-Semicarbazone Ligand

Copper–semicarbazone ligands have been extensively investigated for several medicinal applications. In this contribution, a novel copper(II) complex with a pyridoxal–semicarbazone ligand, [Cu(PLSC)Cl(H2O)](NO3)(H2O), was synthesized and characterized by X-ray crystallography, elemental analysis, UV-VIS, and FTIR spectroscopies. The stabilization interactions within the structure were assessed using the Hirshfeld surface analysis. The crystallographic structure was optimized at the B3LYP/6-311++G(d,p)(H,C,N,O)/LanL2DZ(Cu) level of theory. A comparison between the experimental and theoretical bond lengths and angles was undertaken to verify the applicability of the selected level of theory. The obtained high correlation coefficients and low mean absolute errors confirmed that the optimized structure is suitable for further investigating the interactions between donor atoms and copper, along with the interactions between species in a neutral complex, using the Quantum Theory of Atoms in Molecules approach. The electrostatic potential surface map was used to reveal distinct charge distributions. The experimental and calculated FTIR spectra were compared, and the most prominent bands were assigned. The interactions with human serum albumin (HSA) were assessed by spectrofluorometric titration. The spontaneity of the process was proven, and the thermodynamic parameters of binding were calculated. Molecular docking analysis identified the most probable binding site, providing additional insight into the nature of the interactions.

Cisplatin/Apo-Transferrin Adduct: X-ray Structure and Binding to the Transferrin Receptor 1.

Here, we report the X-ray structure of the adduct formed upon reaction of cisplatin, one of the most prescribed anticancer agents for the clinic treatment of solid tumors, with the apo-form of human serum transferrin (hTF). Two Pt binding sites were identified in both molecules of the adduct present in the crystal asymmetric unit: Pt binds close to the side chains of Met256 and Met499 at the N- and C-lobe, respectively. In the crystal structure, the cisplatin moiety bound to Met256 also interacts with Ser616 from a symmetry related molecule. Structural analyses, together with in solution data, demonstrate that the presence of iron does not affect the ability of hTF to bind cisplatin and that the cisplatin binding does not significantly alter the overall conformation of the different forms of the protein that remain able to form a complex with the transferrin receptor 1 (TfR1). These data suggest that the different hTF forms can be used as nanocarriers for targeted (combined) metallodrug delivery.

The Integration of Microwave-Synthesized Silver Colloidal Nanoparticles into Poly (Lactic Acid)-Based Textiles as Antimicrobial Agents via Pre- and Post-Electrospinning Processes.

This study introduces a novel method to enhance the antibacterial functionality of electrospun nanofibrous textiles by integrating silver nanoparticles (AgNPs) into poly (lactic acid) (PLA) fabrics through pre- and post-electrospinning techniques. AgNPs were incorporated into hydrophobic and modified hydrophilic PLA textiles via pre-solution blending and post-solution casting. A PEG-PPG-PEG tri-block copolymer was utilized to enhance hydrophilicity and water stability, while AgNPs served as antibacterial agents. Morphological analyses confirmed uniform, smooth, and beadless nanofibers with diameters between 435 and 823 nm. Energy-dispersive X-ray spectroscopy spectra and elemental analysis verified the successful incorporation of AgNPs, with higher Ag content in the post-electrospinning samples. Contact angle measurements showed an improved hydrophilicity of the modified PLA textiles, absorbing water droplets within 2 s. The X-ray crystallography patterns confirmed the amorphous structures of the PLA and PEG-PPG-PEG, with reduced crystallinity in the samples containing AgNPs. Thermal analysis indicated lower decomposition temperatures for the hydrophilic samples due to the plasticizing effects of PEG-PPG-PEG on PLA. Mechanical testing showed comparable tensile strengths but reduced elongation in the post-treated samples. The antibacterial efficacy was assessed against various bacterial strains, with post-electrospinning AgNP incorporation showing the most effective antibacterial properties. The results indicate that integrating electrospinning and nanofiber modification techniques expands the applications of PLA-based protective fabrics for disabled individuals.

Guanidinium-Stapled Helical Peptides for Targeting Protein-Protein Interactions.

Peptide stapling has emerged as a versatile approach in drug discovery to reinforce secondary structure elements especially α-helices and improve properties of linear bioactive peptides. Inspired by the prevalence of arginine in protein-protein and protein-DNA interfaces, we investigated guanidinium-stapling as a means to constrain helical peptides. Guanidinium stapling was readily achieved on solid support, utilizing two orthogonally protected lysine or unatural α-amino acid residues with an amino function. This method allows for easy modulation of the nature and size of the staple as well as helix propensity. Evaluating a set of guanidinium-stapled peptides for their interaction with different protein targets identified several binders with increased target affinity. X-ray structure determination of four complexes revealed that all stapled peptides adopt a helical conformation upon protein binding. Notably, the disubstituted guanidinium generally exhibits a distinct cis/trans conformation and, in one instance, retains a conserved hydrogen bond with the protein surface. By identifying, for the first time, the guanidinium moiety as an effective helical peptide stapling group, this research significantly expands the repertoire of α-helix stapling techniques for the creation of useful protein mimics.

Depsides from Origanum dictamnus and Satureja pilosa as selective inhibitors of carbonic anhydrases: Isolation, structure elucidation, X-ray crystallography.

In this study, four depsides were isolated from Origanum dictamnus L. and Satureja pilosa Velen. medicinal plants and their structures were assessed by means of one-dimensional (1D)- and two-dimensional (2D)-nuclear magnetic resonance, high resolution mass spectrometry, and electronic circular dichroism analyses. The compound 1, herein reported for the first time, salvianolic acid P 2, clinopodic acid I 3, and clinopodic acid O 4 were all profiled in vitro on a panel of human (h) expressed carbonic anhydrases (CAs; EC 4.2.1.1) and preferential inhibition for the tumor-associated human carbonic anhydrase (hCA) IX and hCA XII over the constitutively expressed hCA I and hCA II isoforms was observed. X-ray crystallography allowed us to assess the binding mode of salvianolic acid P 2 to hCA II. The compounds exhibited significant cytotoxic effects on the human triple-negative breast cancer cell line MDA-MB-231, suggesting that this class of depsides are promising molecules for future investigation.

Analytical Techniques for Characterizing the Composition and Structure of Complex Biomolecules

The study explores analyzing complex biomolecules is essential for advancing our understanding of biological systems and their role in health and disease. This abstract provides an overview of analytical techniques used to characterize the composition and structure of these intricate biomolecules. One crucial technique is mass spectrometry, which enables the precise determination of a biomolecule's molecular weight and the identification of its constituent atoms and functional groups. Liquid chromatography-mass spectrometry (LC-MS) and tandem mass spectrometry (MS/MS) are commonly employed for this purpose. These methods are particularly useful for analyzing proteins, nucleic acids, lipids, and carbohydrates. Nuclear magnetic resonance (NMR) spectroscopy is another indispensable tool for characterizing biomolecular structures. It provides atomic-level insights into three-dimensional structures, dynamics, and interactions. By measuring chemical shifts and coupling constants, NMR allows researchers to deduce the connectivity and conformation of complex biomolecules. X-ray crystallography, although mainly applied to proteins and larger biomolecules, provides high-resolution structural information. It involves the formation of crystalline structures that diffract X-rays, yielding detailed atomic structures. Electron microscopy, including cry-electron microscopy (cry-EM), is pivotal for visualizing macromolecular complexes and subcellular structures. It offers structural information at nanometre to near-atomic resolution, enabling the study of protein-protein interactions and organelle architecture. Infrared spectroscopy (IR) and circular dichroism (CD) spectroscopy are employed to probe biomolecule secondary structures, such as alpha-helices and beta-sheets, based on their unique vibrational and optical properties. These analytical techniques, when used in combination, provide a comprehensive view of the composition, conformation, and interactions of complex biomolecules. Their integration advances our understanding of fundamental biological processes and facilitates drug discovery and the development of therapeutic interventions.

Enabling structural biological electron paramagnetic resonance spectroscopy in membrane proteins through spin labelling.

Pulsed dipolar electron paramagnetic resonancespectroscopy (PDS), combined with site-directed spin-labelling, represents a powerful tool for the investigation of biomacromolecules, emerging as a keystone approach in structural biology. Increasingly, PDS is applied to study highly complex integral membrane protein systems, such as mechanosensitive ion channels, transporters, G-protein coupled receptors, ion pumps, and outer membrane proteins elucidating their dynamics and revealing conformational ensembles. Indeed, PDS offers a platform to study intermediate or lowly-populated states that are otherwise invisible to other modern methods, such as X-ray crystallography, cryo-EM, and hydrogen-deuterium exchange-mass spectrometry. Importantly, advances in spin labelling strategies welcome a new era of membrane protein investigation under near-native or in-cell conditions. Here, we review recent integral membrane protein PDS applications, and highlight well-suited, emerging spin labelling strategies that show promise for future studies.

Identification of Cysteine Metabolism Regulator (CymR)-Derived Pentapeptides as Nanomolar Inhibitors of Staphylococcus aureus O-Acetyl-l-serine Sulfhydrylase (CysK).

The pathway of bacterial cysteine biosynthesis is gaining traction for the development of antibiotic adjuvants. Bacterial cysteine biosynthesis is generally facilitated by two enzymes possessing O-acetyl-l-serine sulfhydrylases (OASS), CysK and CysM. In Staphylococcus aureus, there exists a single OASS homologue, SaCysK. Knockout of SaCysK was found to increase sensitivity to oxidative stress, making it a relevant target for inhibitor development. SaCysK also forms two functional complexes via interaction with the preceding enzyme in the pathway serine acetyltransferase (CysE) or the transcriptional regulator of cysteine metabolism (CymR). These interactions occur through insertion of a C-terminal peptide of CysE or CymR into the active site of SaCysK, inhibiting OASS activity, and therefore represent an excellent starting point for developing SaCysK inhibitors. Here, we detail the characterization of CysE and CymR-derived C-terminal peptides as inhibitors of SaCysK. Using a combination of X-ray crystallography, surface plasmon resonance, and enzyme inhibition assays, it was determined that the CymR-derived decapeptide forms extensive interactions with SaCysK and acts as a potent inhibitor (KD = 25 nM; IC50 = 180 nM), making it a promising lead for the development of SaCysK inhibitors. To understand the determinants of this high-affinity interaction, the structure-activity relationships of 16 rationally designed peptides were also investigated. This identified that the C-terminal pentapeptide of CymR facilitates the high-affinity interaction with SaCysK and that subtle structural modification of the pentapeptide is possible without impacting potency. Ultimately, this work identified CymR pentapeptides as a promising scaffold for the development of antibiotic adjuvants targeting SaCysK.

Multiple Binding Modes of Inhibitors to Human Carbonic Anhydrases: An Update on the Design of Isoform-Specific Modulators of Activity.

Human carbonic anhydrases (hCAs) are widespread zinc enzymes that catalyze the hydration of CO2 to bicarbonate and a proton. Currently, 15 isoforms have been identified, of which only 12 are catalytically active. Given their involvement in numerous physiological and pathological processes, hCAs are recognized therapeutic targets for the development of inhibitors with biomedical applications. However, despite massive development efforts, very few of the presently available hCA inhibitors show selectivity for a specific isoform. X-ray crystallography is a very useful tool for the rational drug design of enzyme inhibitors. In 2012 we published in Chemical Reviews a highly cited review on hCA family (Alterio, V. et al. Chem Rev. 2012, 112, 4421-4468), analyzing about 300 crystallographic structures of hCA/inhibitor complexes and describing the different CA inhibition mechanisms existing up to that date. However, in the period 2012-2023, almost 700 new hCA/inhibitor complex structures have been deposited in the PDB and a large number of new inhibitor classes have been discovered. Based on these considerations, the aim of this Review is to give a comprehensive update of the structural aspects of hCA/inhibitor interactions covering the period 2012-2023 and to recapitulate how this information can be used for the rational design of more selective versions of such inhibitors.

Beyond expectations: the development and biological activity of cytokinin oxidase/dehydrogenase inhibitors.

Cytokinins are one of the main groups of plant hormones that regulate growth and development of plants. Cytokinin oxidase/dehydrogenase (CKX) is an enzyme that rapidly and irreversibly degrades cytokinins and thus directly affects their concentration and physiological effect. Genetically modified plants with reduced CKX activity in the shoot, i.e. with a higher concentration of cytokinins, showed e.g. increased tolerance to drought stress, formed larger inflorescences and had higher grain yield. For these reasons, chemical compounds capable of inhibiting the CKX activity (CKX inhibitors) were sought. First, they were identified among strong synthetic cytokinins, but their inhibitory activity was low. The trend has been to develop potent CKX inhibitors with minimal intrinsic cytokinin activity in the hope of avoiding the negative effect of cytokinins on root growth. Cloning CKX, production of key recombinant enzymes from Arabidopsis (AtCKX2) and maize (ZmCKX1 and ZmCKX4a), development of screening bioassays and progress in X-ray crystallography and synthetic organic chemistry led to extensive progress in the development of these compounds. Currently, the most suitable CKX inhibitors are seeking their application in research and the commercial sphere in two main areas - plant tissue cultures and agriculture. The key milestones that preceded it are summarized in this review.

Synthesis, structure, Hirshfeld surface analysis, and molecular docking studies of the cocrystal between the Cu(II) complex of salicylic acid and uncoordinated piracetam.

The cocrystal (or supramolecular complex) between the Cu(II) complex of salicylic acid and uncoordinated piracetam has been synthesized. Its structure is characterized by elemental analysis, FT-IR, UV-Vis spectroscopy, and X-ray crystallography. Spectroscopic methods confirm the formation of the metal complex, while X-ray crystallography establishes the molecular and crystal structure of the obtained compound. The Cu(II) complex of salicylic acid (complex molecule) is a symmetric binuclear compound in the form of a "Chinese lantern" and contains 4 salicylic acid and 2 water molecules. It interacts with uncoordinated piracetam through a complicated system of hydrogen bonds. However, according to Hirshfeld surface analysis, the contribution of the O•••H/H•••O contacts is only 24.9%, while H•••H and H•••C/C•••H contacts account for 67.5%, indicating that intermolecular interactions are mainly hydrophobic. In silico (molecular docking) studies of the cocrystal, the complex molecule, and piracetam's antifungal, antibacterial, and antiviral activities confirm that the complex molecule demonstrates enhanced biological activities; practically, the inactive piracetam improved all tested types of bioactivities through cocrystal formation. For example, the binding energy in the case of anti-COVID activity is improved from -10.34 to -11.40 kcal/mol. Thus, cocrystal formation based on metal complexes and inactive organic compounds may be promising in drug design.

New lanthanum (III) complexes containing azaphosphor β-diketon and diimine ligands: Synthesis, crystallography, morphology properties, DNA binding, DNA cleavage, and DFT calculation.

Two octa-coordinated lanthanum (III) complexes of deprotonated azaphosphor β-diketon and diimine ligands, [LnL3Q] (L=[Cl2CHC(O)NP(O)(NC6H12)2], Q=Phen (C1) and Bipy (C2)), were synthesized and characterized by elemental analysis, IR, and NMR spectra. X-ray crystallography revealed a distorted tetragonal antiprism LaO6N2 coordination geometry around the lanthanum atom in both compounds. Nano-sized complexes (Ć1 and Ć2) were synthesized via a sonochemical process and analyzed using SEM and XRPD. TGA-DTA analysis were performed on complexes in both bulk and nano scales. Redox behavior was also examined by cyclic voltammetry. The interaction between the complexes and calf thymus DNA (ct-DNA) was investigated using UV-Vis spectroscopy, fluorescence titration, viscosity measurements, and gel electrophoresis. C2 and Ć2 likely intercalate between DNA base pairs through van der Waals forces and hydrogen bonding, whereas C1 and Ć1 interact with DNA via groove binding. Further, result indicated the apparent association constant (Kapp) in the range of 4.53×104M-1-26.86×104M-1 with the highest value for nanocomplex Ć2. Fluorescence studies revealed dynamic and static quenching for C1, while the other compounds followed a static quenching process. Hirshfeld surface analysis and the NCI method were employed to demonstrate how non-covalent interactions influence the crystal packing through intermolecular interactions.

Impact of Intracellular Proteins on μ-Opioid Receptor Structure and Ligand Binding.

Chronic pain is a prevalent problem affecting approximately one out of every five adults in the U.S. The most effective way to treat chronic pain is with opioids, but they cause dangerous side effects such as tolerance, addiction, and respiratory depression, which makes them quite deadly. Opioids, such as fentanyl, target the μ-opioid receptor (MOR), which can then bind to the intracellular Gi protein or the β-arrestin protein. The Gi pathway is primarily responsible for pain relief and potential side effects, but the β-arrestin pathway is chiefly responsible for the unwanted side effects. Ideally, an effective pain medication without side effects would bind to MOR, which would bias signaling solely through the Gi pathway. We used the Bio3D library to conduct principal component analysis to compare the cryo-electron microscopy MOR structures in complex with the Gi versus an X-ray crystallography MOR structure with a nanobody acting as a Gi mimic. Our results agree with a previous study by Munro, which concluded that nanobody-bound MOR is structurally different than Gi-bound MOR. Furthermore, we investigated the structural diversity of opioids that can bind to MOR. Quantum mechanical calculations show that the low energy solution structures of fentanyl differ from the one bound to MOR in the experimental structure, and pKa calculations reveal that fentanyl is protonated in aqueous solution. Glide docking studies show that higher energy structures of fentanyl in solution form favorable docking complexes with MOR. Our calculations show the relative abundance of each fentanyl conformation in solution as well as the energetic barriers that need to be overcome to bind to MOR. Docking studies confirm that multiple fentanyl conformations can bind to the receptor. Perhaps a variety of conformations of fentanyl can stabilize multiple conformations of the MOR, which can explain why fentanyl can induce different intracellular signaling and multiple physiological effects.