Relative Affinities Research Articles

Flexibility of Binding Site is Essential to the Ca2+ Selectivity in EF-Hand Calcium-Binding Proteins.

High binding affinity and selectivity of metal ions are essential to the function of metalloproteins. Thus, understanding the factors that determine these binding characteristics is of major interest for both fundamental mechanistic investigations and guiding of the design of novel metalloproteins. In this work, we perform QM cluster model calculations and quantum mechanics/molecular mechanics (QM/MM) free energy simulations to understand the binding selectivity of Ca2+ and Mg2+ in the wild-type carp parvalbumin and its mutant. While a nonpolarizable MM model (CHARMM36) does not lead to the correct experimental trend, treatment of the metal binding site with the DFTB3 model in a QM/MM framework leads to relative binding free energies (ΔΔGbind) comparable with experimental data. For the wild-type (WT) protein, the calculated ΔΔGbind is ∼6.6 kcal/mol in comparison with the experimental value of 5.6 kcal/mol. The good agreement highlights the value of a QM description of the metal binding site and supports the role of electronic polarization and charge transfer to metal binding selectivity. For the D51A/E101D/F102W mutant, different binding site models lead to considerable variations in computed binding affinities. With a coordination number of seven for Ca2+, which is shown by QM/MM metadynamics simulations to be the dominant coordination number for the mutant, the calculated relative binding affinity is ∼4.8 kcal/mol, in fair agreement with the experimental value of 1.6 kcal/mol. The WT protein is observed to feature a flexible binding site that accommodates a range of coordination numbers for Ca2+, which is essential to the high binding selectivity for Ca2+ over Mg2+. In the mutant, the E101D mutation reduces the flexibility of the binding site and limits the dominant coordination number of Ca2+ to be seven, thereby leading to reduced binding selectivity against Mg2+. Our results highlight that the binding selectivity of metal ions depends on both the structural and dynamical properties of the protein binding site.

Analysing the genetic diversity and population structure of five native Turkish cattle breeds using SNP data.

The conservation and sustainable utilization of cattle genetic resources necessitate a comprehensive understanding of their genetic diversity and population structure. This study provides an analysis of five native Turkish cattle breeds: Anatolian Black (ANB), Turkish Grey (TUR), Anatolian Southern Yellow (ASY), East Anatolian Red (EAR), and South Anatolian Red (SAN) using 50 K SNP data. These breeds were compared with three European breeds, Simmental (SIM), Holstein (HOL), and Jersey (JER), and three Asian Zebu breeds: Arabic Zebu (ZAR), Nelore (NEL), and Red Sindhi (RSI). Genetic diversity indices demonstrated moderate heterogeneity among the breeds, with TUR exhibiting the highest observed heterozygosity (Ho = 0.35). Wright's Fst values indicated significant genetic differentiation, particularly between Turkish breeds and both European (Fst = 0.035-0.071) and Asian breeds (Fst = 0.025-0.150). Principal component analysis distinguished the unique genetic profiles of each breed cluster. Admixture analysis revealed degrees of shared genetic ancestry, suggesting historical gene flow between Turkish, European, and Asian breeds. Analysis of molecular variance (AMOVA) attributed approximately 58% of the variation to population differences. Nei's genetic distances highlighted the closer genetic relatedness within Turkish breeds (distance ranges between 0.032 and 0.046) and suggested a more relative affinity of TUR with European breeds. The study's phylogenetic assessments elucidate the nuanced genetic relationships among these breeds, with runs of homozygosity (ROH) analysis indicating patterns of ancestral relatedness and moderate levels of inbreeding, particularly evident in Turkish breeds. Our findings provide valuable insights into the genetic landscape of Turkish cattle, offering a crucial foundation for informed conservation and breeding strategies aimed at preserving these breeds' genetic integrity and heritage.

Anticonvulsant effect of (±) citronellal possibly through the GABAergic and voltage-gated sodium channel receptor interaction pathways: In vivo and in silico studies

This study aimed to investigate the anticonvulsant effects of citronellal (CIT) and possible underlying mechanisms through an isoniazid (INH)-induced seizure (convulsion) via in vivo and in silico studies. For this, convulsions were induced by the oral administration of INH (300 mg/kg) to the mice. The animals were treated orally with different doses of CIT (50, 100, and 200 mg/kg). Vehicle served as a negative control (NC), while diazepam (DZP) (2 mg/kg) and carbamazepine (CAR) (80 mg/kg) were provided (p.o.) as positive controls (PC). A combination therapy of CIT (middle dose) with DZP and CAR was also given to two separate groups of animals to estimate the synergistic or antagonistic effects. Molecular docking and visualization of ligand-receptor interactions are also estimated through different computational tools. The results of the in vivo study showed that CIT dose-dependently significantly (p < 0.05) exhibited a higher onset of seizures while reducing the frequency and duration of seizures in mice compared to the NC group. Besides these, in combination therapy, CIT significantly antagonized the activity of CAR and DZP, leading to a reduction in the onset of seizures and an increase in their frequency and duration compared to treatment with CAR and DZP alone. Additionally, molecular docking revealed that the CIT exhibited a moderate binding affinity (−5.8 kcal/mol) towards the GABAA receptor and a relative binding affinity (−5.3 kcal/mol) towards the voltage-gated sodium channel receptor by forming several bonds. In conclusion, CIT showed moderate anticonvulsant activity in INH-induced convulsion animals, possibly by enhancing GABAA receptor activity and inhibiting the voltage-gated sodium channel receptor.

General synthesis and atomic arrangement identification of ordered Bi-Pd intermetallics with tunable electrocatalytic CO2 reduction selectivity.

Intermetallic compounds (IMCs) with fixed chemical composition and ordered crystallographic arrangement are highly desirable platforms for elucidating the precise correlation between structures and performances in catalysis. However, diffusing a metal atom into a lattice of another metal to form a controllably regular metal occupancy remains a huge challenge. Herein, we develop a general and tractable solvothermal method to synthesize the Bi-Pd IMCs family, including Bi2Pd, BiPd, Bi3Pd5, Bi2Pd5, Bi3Pd8 and BiPd3. By employing electrocatalytic CO2 reduction as a model reaction, we deeply elucidated the interplay between Bi-Pd IMCs and key intermediates. Specific surface atomic arrangements endow Bi-Pd IMCs different relative surface binding affinities and adsorption configuration for *OCHO, *COOH and *H intermediate, thus exhibiting substantially selective generation of formate (Bi2Pd), CO (BiPd3) and H2 (Bi2Pd5). This work provides a comprehensive understanding of the specific structure-performance correlation of IMCs, which serves as a valuable paradigm for precisely modulating catalyst material structures.

Investigating vulnerability of the conserved SARS-CoV-2 spike's heptad repeat 2 as target for fusion inhibitors using chimeric miniproteins

Inhibition of SARS-CoV-2 membrane fusion is a highly desired target to combat COVID-19. The interaction between the spike's heptad repeat (HR) regions 1 (HR1) and 2 (HR2) is a crucial step during the fusion process and these highly conserved HR regions constitute attractive targets for fusion inhibitors. However, the relative importance of each subregion of the long HR1-HR2 interface for viral inhibition remains unclear. Here, we designed, produced, and characterized a series of chimeric miniproteins that mimic two different half subdomains of HR1. The proteins were designed as single polypeptide chains that spontaneously fold into antiparallel trimeric helical bundles aimed at structurally imitate the molecular surface of each HR1 half subregion. All the miniproteins folded stably as helical structures and could bind complementary HR2 peptides with moderate affinity. However, only the miniproteins mimicking the N-terminal HR1 half subdomain, but not those imitating C-terminal one, could inhibit cell infection by SARS-COV-2 real viruses in cell cultures. Most interestingly, the inhibitory activity of the miniproteins correlated with their structural stability, but not with their relative binding affinity for HR2 peptides. These results are highly relevant for designing more focused and active fusion inhibitors targeting the highly conserved HR2 region of the Spike.

Computational Workflow for Refining AlphaFold Models in Drug Design Using Kinetic and Thermodynamic Binding Calculations: A Case Study for the Unresolved Inactive Human Adenosine A3 Receptor.

A structure-based drug design pipeline that considers both thermodynamic and kinetic binding data of ligands against a receptor will enable the computational design of improved drug molecules. For unresolved GPCR-ligand complexes, a workflow that can apply both thermodynamic and kinetic binding data in combination with alpha-fold (AF)-derived or other homology models and experimentally resolved binding modes of relevant ligands in GPCR-homologs needs to be tested. Here, as test case, we studied a congeneric set of ligands that bind to a structurally unresolved G protein-coupled receptor (GPCR), the inactive human adenosine A3 receptor (hA3R). We tested three available homology models from which two have been generated from experimental structures of hA1R or hA2AR and one model was a multistate alphafold 2 (AF2)-derived model. We applied alchemical calculations with thermodynamic integration coupled with molecular dynamics (TI/MD) simulations to calculate the experimental relative binding free energies and residence time (τ)-random accelerated MD (τ-RAMD) simulations to calculate the relative residence times (RTs) for antagonists. While the TI/MD calculations produced, for the three homology models, good Pearson correlation coefficients, correspondingly, r = 0.74, 0.62, and 0.67 and mean unsigned error (mue) values of 0.94, 1.31, and 0.81 kcal mol-1, the τ-RAMD method showed r = 0.92 and 0.52 for the first two models but failed to produce accurate results for the multistate AF2-derived model. With subsequent optimization of the AF2-derived model by reorientation of the side chain of R1735.34 located in the extracellular loop 2 (EL2) that blocked ligand's unbinding, the computational model showed r = 0.84 for kinetic data and improved performance for thermodynamic data (r = 0.81, mue = 0.56 kcal mol-1). Overall, after refining the multistate AF2 model with physics-based tools, we were able to show a strong correlation between predicted and experimental ligand relative residence times and affinities, achieving a level of accuracy comparable to an experimental structure. The computational workflow used can be applied to other receptors, helping to rank candidate drugs in a congeneric series and enabling the prioritization of leads with stronger binding affinities and longer residence times.

Cellular localization and potential ligands of a novel scavenger receptor class B/CD36 protein homolog (Pt-SRB2) identified in the marine crab, Portunustrituberculatus

The scavenger receptor class B family proteins (SRB) are multiligand membrane receptor proteins. Herein, a novel SRB homolog (Pt-SRB2) was identified in Portunus trituberculatus. The open reading frame of Pt-SRB2 was predicted to encode 520 amino acid residues comprising a typical CD36 domain. Phylogenetic analysis showed that Pt-SRB2 distinctly clustered with the SRB homologs of most crustaceans and Drosophila but was separate from all vertebrate CD36/SRB. Semi-quantitative and Real-time quantitative PCR revealed that the abundance of Pt-SRB2 transcripts was the highest in hepatopancreas than in other tested tissues. Overexpressed Pt-SRB2 was distributed primarily in the cell membrane and cytoplasm of HEK293T or Drosophila Schneider 2 cells. In crab hemocytes, Pt-SRB2 was distributed primarily in the cell membrane by immunofluorescence staining. In addition, the immunofluorescence staining showed that green fluorescence signals were mainly located in the inner lumen membrane of the hepatopancreatic tubules. Moreover, solid-phase enzyme-linked immunosorbent assay revealed that rPt-SRB2-L exhibited relative high affinity with lipopolysaccharides, and relative moderate binding affinity with lipoteichoic acid or peptidoglycan. Of note, rPt-SRB2-L showed high binding affinity with eicosapentaenoic acid among a series of long-chain polyunsaturated fatty acids. Taken together, this study provided valuable data for understanding the functions of the crab CD36/SRB.

Synthesis and biological evaluation of novel D-ring fused steroidal N(2)-substituted-1,2,3-triazoles.

In this study, a series of 13 new D-ring fused steroidal N(2)-substituted-1,2,3-triazoles were synthesized, characterized and evaluated for their biological activities. The relative binding affinities of the synthesized compounds for the ligand-binding domains of estrogen receptors α and β, androgen receptor and glucocorticoid receptor demonstrated that androstane derivatives 3a and 3h and estratriene derivative 4e showed highly specific and strong binding affinity for estrogen receptor β, while 3b, 3e, 4a and 4b displayed high binding affinity for the glucocorticoid receptor. The synthesized compounds were tested for their ability to inhibit aldo-keto reductases 1C3 and 1C4 in vitro by monitoring NADPH consumption using fluorescence spectroscopy. The most potent aldo-keto reductase 1C3 inhibitors were compounds 3h (71.17%) and 3f (69.9%). Moreover, a molecular docking study was carried out for compounds 3f and 3h against aldo-keto reductase 1C3 and results showed that compounds 3h and 3f could bind in the same site and orientation as EM1404. However, polar atoms in the triazole group enable additional hydrogen bonding deeper in SP1 with Tyr319, Tyr216 and the NADP+ cofactor, which are not visible in the AKR1C3-EM1404 crystal structure. The synthesized compounds were screened for their anticancer activity against four cancer cell lines. Compound 3f demonstrated moderate toxic effects across various cancer types, while displaying lower toxicity towards the healthy cell line. In summary, our findings indicate that N(2)-substituted-1,2,3-triazoles are high-affinity ligands for estrogen receptor β and glucocorticoid receptor, inhibitors of aldo-keto reductase 1C3 enzyme, and exhibit antiproliferative effects against cancer cells, suggesting that they could serve as scaffolds for anticancer drug development.

Correlated proton dynamics in hydrogen bonding networks: the benchmark case of 3-hydroxyglutaric acid.

Proton and hydrogen-bonded networks sustain a broad range of structural and charge transfer processes in supramolecular materials. The modelling of proton dynamics is however challenging and demands insights from prototypical benchmark systems. The intramolecular H-bonding networks induced by either protonation or deprotonation of 3-hydroxyglutaric acid provide intriguing case studies of correlated proton dynamics. The vibrational signatures associated with the fluxional proton bonding and its coupling with the hydroxyglutaric backbone are investigated here with infrared action ion spectroscopy experiments and Born-Oppenheimer molecular dynamics (BOMD) computations. Despite the formally similar symmetry of protonated and deprotonated hydroxyglutaric acid, the relative proton affinities of the oxygen centers of the carboxylic and carboxylate groups with respect to that of the central hydroxyl group lead to distinct proton dynamics. In the protonated acid, a tautomeric arrangement of the type HOCO·[HOH]+·OCOH is preferred with the proton binding tighter to the central hydroxyl moiety and the electronic density being shared between the two nearly symmetric H-bonds with the carboxylic end groups. In the deprotonated acid, the asymmetric [OCO]-·HO·HOCO configuration is more stable, with a stronger H-bonding on the bare carboxylate end. Both systems display active backbone dynamics and concerted Grothuss-like proton motions, leading to diffuse band structures in their vibrational spectra. These features are accurately reproduced by the BOMD computations.

Roles of β-adrenoceptor Subtypes and Therapeutics in Human Cardiovascular Disease: Heart Failure, Tachyarrhythmias and Other Cardiovascular Disorders.

β-Adrenoceptors (β-ARs) provide an important therapeutic target for the treatment of cardiovascular disease. Three β-ARs, β1-AR, β2-AR, β3-AR are localized to the human heart. Activation of β1-AR and β2-ARs increases heart rate, force of contraction (inotropy) and consequently cardiac output to meet physiological demand. However, in disease, chronic over-activation of β1-AR is responsible for the progression of disease (e.g. heart failure) mediated by pathological hypertrophy, adverse remodelling and premature cell death. Furthermore, activation of β1-AR is critical in the pathogenesis of cardiac arrhythmias while activation of β2-AR directly influences blood pressure haemostasis. There is an increasing awareness of the contribution of β2-AR in cardiovascular disease, particularly arrhythmia generation. All β-blockers used therapeutically to treat cardiovascular disease block β1-AR with variable blockade of β2-AR depending on relative affinity for β1-AR vs β2-AR. Since the introduction of β-blockers into clinical practice in 1965, β-blockers with different properties have been trialled, used and evaluated, leading to better understanding of their therapeutic effects and tolerability in various cardiovascular conditions. β-Blockers with the property of intrinsic sympathomimetic activity (ISA), i.e. β-blockers that also activate the receptor, were used in the past for post-treatment of myocardial infarction and had limited use in heart failure. The β-blocker carvedilol continues to intrigue due to numerous properties that differentiate it from other β-blockers and is used successfully in the treatment of heart failure. The discovery of β3-AR in human heart created interest in the role of β3-AR in heart failure but has not resulted in therapeutics at this stage.

An In Silico Investigation of the Molecular Interactions between Volatile Anesthetics and Actin.

Volatile anesthetics (VAs) are medicinal chemistry compounds commonly used to enable surgical procedures for patients who undergo painful treatments and can be partially or fully sedated, remaining in an unconscious state during the operation. The specific molecular mechanism of anesthesia is still an open issue, but scientific evidence supports the hypothesis of the involvement of both putative hydrophobic cavities in membrane receptors as binding pockets and interactions between anesthetics and cytoplasmic proteins. Previous studies demonstrated the binding of VAs to tubulin. Since actin is the other major component of the cytoskeleton, this study involves an investigation of its interactions with four major anesthetics: halothane, isoflurane, sevoflurane, and desflurane. Molecular docking was implemented using the Molecular Operating Environment (MOE) software (version 2022.02) and applied to a G-actin monomer, extrapolating the relative binding affinities and root-mean-square deviation (RMSD) values. A comparison with the F-actin was also made to assess if the generally accepted idea about the enhanced F-to-G-actin transformation during anesthesia is warranted. Overall, our results confirm the solvent-like behavior of anesthetics, as evidenced by Van der Waals interactions as well as the relevant hydrogen bonds formed in the case of isoflurane and sevoflurane. Also, a comparison of the interactions of anesthetics with tubulin was made. Finally, the short- and long-term effects of anesthetics are discussed for their possible impact on the occurrence of mental disorders.

25 Years Responding to Respiratory and Other Viruses with Mass Spectrometry.

This review article presents the development and application of mass spectrometry (MS) approaches, developed in the author's laboratory over the past 25 years, to detect; characterise, type and subtype; and distinguish major variants and subvariants of respiratory viruses such as influenza and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). All features make use of matrix-assisted laser desorption ionisation (MALDI) mass maps, recorded for individual viral proteins or whole virus digests. A MALDI-based immunoassay in which antibody-peptide complexes were preserved on conventional MALDI targets without their immobilisation led to an approach that enabled their indirect detection. The site of binding, and thus the molecular antigenicity of viruses, could be determined. The same approach was employed to study antivirals bound to their target viral protein, the nature of the binding residues, and relative binding affinities. The benefits of high-resolution MS were exploited to detect sequence-conserved signature peptides of unique mass within whole virus and single protein digests. These enabled viruses to be typed, subtyped, their lineage determined, and variants and subvariants to be distinguished. Their detection using selected ion monitoring improved analytical sensitivity limits to aid the identification of viruses in clinical specimens. The same high-resolution mass map data, for a wide range of viral strains, were input into a purpose-built algorithm (MassTree) in order to both chart and interrogate viral evolution. Without the need for gene or protein sequences, or any sequence alignment, this phylonumerics approach also determines and displays single-point mutations associated with viral protein evolution in a single-tree building step.

Unusual temperature-dependent volume properties of water as a solute in tertiary butylamine at ambient pressure

Densities of water solutions in tert-butylamine (t-BuNH2) with the solute molality from ca. (0.015 to 0.35) mol∙(kg solvent)−1 were measured at six temperatures, from T = (278.15 to 303.15) K, and p ∼ 0.1 MPa. The uncertainty in density measurements did not exceed 0.03 kg m−3. The standard (apparent at infinite dilution) molar volumes and expansibilities of water as a solute in t-BuNH2 were calculated. The origins for the phenomenon of the temperature-induced relative partial molar isobaric compaction of a solute (PMICS) in the system under study were discussed based on Ben-Naim’s concept of the “relative affinity parameter”.

Comparing in vitro affinity measurements of antibodies to TfR1: Surface plasmon resonance versus on-cell affinity

Despite years of utilizing the transferrin receptor 1 (TfR1) to transport large biomolecules into the brain, there is no consensus on how to optimally measure affinity to it. The aim of this study was to compare different methods for measuring the affinities of anti-TfR1 antibodies.Antibodies 15G11, OX26 and 8D3 are known to successfully carry large biologics across the blood-brain barrier in humans, rats, and mice, respectively. The affinity to their respective species of TfR1 was measured with different surface plasmon resonance setups in Biacore and an on-cell assay.When the antibody was captured and TfR1 was the analyte, the dissociation in Biacore was very slow. The dissociation was faster when the antibody was the analyte and TfR1 was the ligand. The Biacore setup with capture of N-terminal FLAG-tag TfR1 yielded the most similar apparent affinities as the cell assay.In conclusion, it is important to evaluate assay parameters including assay orientation, surface capture method, and antibody-format when comparing binding kinetics for TfR1 antibodies. Although it seems possible to determine relative affinities of TfR1 antibodies using the methods described here, both the FLAG-tag TfR1 capture setup and cell assays likely yield apparent affinities that are most translatable in vivo.

Ties That Blind: A Longitudinal Study on Consanguinity and Congenital Disorders in Kabirwala, Pakistan

Consanguineous marriage, defined as marriage between close relatives, is a prevalent practice in many traditional societies. It is commonly perceived to secure property rights, maintain social cohesion, and fortify kinship structures. However, consanguineous marriages are also associated with an increased risk of inbreeding and consequent chromosomal disorders. Pakistan has one of the highest rates of consanguineous marriage worldwide, with an estimated 60% of all marriages occurring between close relatives. This study focuses on the persistence of consanguinity in Kabirwala, Pakistan, a town in the Punjab province. It investigates the trend of consanguinity and relative affinity according to generations in Kabirwala. It also observes the effects of modernization on consanguinity and explores the reasons behind the practice from the respondents' perspectives. The study used a longitudinal qualitative design, conducting in-depth interviews with the same participants (N=24 couples) over 15 years. Findings indicate that consanguinity is still prevalent in Kabirwala, with 77% of marriages between cousins. The study also found that the practice is rooted in traditional knowledge frameworks that link consanguinity to congenital disorders. However, modernization has led to a decline in consanguineous marriage among younger generations.

One Platform Comparison of Polymeric and Lipidic Nanoparticles for the Delivery of Amphotericin B.

Amphotericin B (AmB) is a membrane-acting antibiotic used for the treatment of fungal and protozoal infections. AmB exists in various molecular forms, i.e., monomeric, super-aggregated, and oligomeric forms, where oligomeric forms are highly toxic because of their relative affinity toward cholesterol present over human cell membrane. Hence, the objective of our research work was to study the aggregation state of AmB in two different nanoformulations, i.e., solid lipid nanoparticles (SLNs) and zein-based nanoparticles (PNPs), with the aim of enhancing the fraction of less toxic form of AmB, and a comparative study was performed. The zein and glyceryl monostearate can intercalate the polyenic domain of AmB and thereby hinder the hydrophobic attractions between the AmB molecules, which allows their existence in monomeric forms. The particle size of AmB-SLNs and AmB-PNPs were 378.90 ± 9.50 nm and 184.90 ± 6.00 nm, while zeta potential was -34.97 ± 0.51 mV and +28.93 ± 2.29 mV, respectively. In vitro release studies showed more controlled release of AmB from PNPs (52.48 ± 1.07%) as compared to SLNs (86.33 ± 0.93%). The predominant aggregation state of AmB in both formulations was determined by UV-visible and circular dichroism spectrophotometry, where a higher degree of monomerization of AmB was reported in AmB-SLNs as compared to AmB-PNPs. Toxicity of the nanoformulations was evaluated through hemolysis test, where the results suggested that AmB-SLNs and AmB-PNPs were less hemolytic as compared to pure AmB. The nanoformulations demonstrated the predominant monomeric form of AmB, which may offer higher selectivity index toward microbial membrane.

Effects of cannabinoid agonists and antagonists in male rats discriminating the synthetic cannabinoid AM2201

The synthetic forms of delta-9-tetrahydrocannabinol (Δ9-THC), dronabinol or nabilone, have been approved to treat several indications. However, due to safety concerns their clinical utility remains limited. Consequently, there is a need for developing cannabinoid (CB) ligands that display better behavioral pharmacological profiles than Δ9-THC. Here, we utilized drug discrimination methods to compare the interoceptive effects of CB ligands that vary in potency, efficacy, and selectivity at the CB receptors, including two ligands, AM411 and AM4089, that show CB1 partial agonist-like actions in vitro. Male rats were trained to discriminate 0.1 mg/kg AM2201 from saline under a fixed-ratio (FR) 10 response schedule of food reinforcement. After establishing AM2201's discriminative-stimulus effects, pretreatment tests with the CB1 antagonist/inverse agonist rimonabant blocked AM2201's effects, whereas the peripherally-restricted antagonist AM6545 had no effect. Next, the generalization profiles of AM411 and AM4089 with CB1 full agonists (JWH-018, CP-55,940, AM8936), partial agonist (Δ9-THC), and non-cannabinoids (fentanyl, atropine) were compared. The CBs either fully (AM2201, CP-55,940, JWH-018, AM8936, Δ9-THC) or partially (AM411, AM4089) substituted for AM2201, whereas fentanyl and atropine did not produce AM2201-like effects. All CB drugs were more potent than Δ9-THC and correlation analysis confirmed that the relative behavioral potencies of CBs corresponded strongly with their relative affinities at the CB1 but not CB2 receptors. Together, our results further demonstrate that AM411 and AM4089 exhibit better pharmacological profiles compared to Δ9-THC, in that they are more potent and display in vivo partial agonist-like actions that are centrally mediated via CB1 receptors.

Comparison of Equilibrium and Nonequilibrium Approaches for Relative Binding Free Energy Predictions.

Alchemical relative binding free energy calculations have recently found important applications in drug optimization. A series of congeneric compounds are generated from a preidentified lead compound, and their relative binding affinities to a protein are assessed in order to optimize candidate drugs. While methods based on equilibrium thermodynamics have been extensively studied, an approach based on nonequilibrium methods has recently been reported together with claims of its superiority. However, these claims pay insufficient attention to the basis and reliability of both methods. Here we report a comparative study of the two approaches across a large data set, comprising more than 500 ligand transformations spanning in excess of 300 ligands binding to a set of 14 diverse protein targets. Ensemble methods are essential to quantify the uncertainty in these calculations, not only for the reasons already established in the equilibrium approach but also to ensure that the nonequilibrium calculations reside within their domain of validity. If and only if ensemble methods are applied, we find that the nonequilibrium method can achieve accuracy and precision comparable to those of the equilibrium approach. Compared to the equilibrium method, the nonequilibrium approach can reduce computational costs but introduces higher computational complexity and longer wall clock times. There are, however, cases where the standard length of a nonequilibrium transition is not sufficient, necessitating a complete rerun of the entire set of transitions. This significantly increases the computational cost and proves to be highly inconvenient during large-scale applications. Our findings provide a key set of recommendations that should be adopted for the reliable implementation of nonequilibrium approaches to relative binding free energy calculations in ligand-protein systems.

Efficient prediction of relative ligand binding affinity in drug discovery.

Efficient prediction of relative ligand binding affinity in drug discovery.

Designing and computational analyzing of chimeric long-lasting GLP-1 receptor agonists for type 2 diabetes

Glucagon-like peptide-1 (GLP-1) is an intestinally derived incretin that plays a vital role in engineering the biological circuit involved in treating type 2 diabetes. Exceedingly short half-life (1–2 min) of GLP-1 limits its therapeutic applicability, and the implication of its new variants is under question. Since albumin-binding DARPin as a mimetic molecule has been reported to increase the serum half-life of therapeutic compounds, the interaction of new variants of GLP-1 in fusion with DARPin needs to be examined against the GLP-1 receptor. This study was aimed to design stable and functional fusion proteins consisting of new protease-resistant GLP-1 mutants (mGLP1) genetically fused to DARPin as a critical step toward developing long-acting GLP-1 receptor agonists. The stability and solubility of the engineered fusion proteins were analyzed, and their secondary and tertiary structures were predicted and satisfactorily validated. Molecular dynamics simulation studies revealed that the predicted structures of engineered fusion proteins remained stable throughout the simulation. The relative binding affinity of the engineered fusion proteins' complex with human serum albumin and the GLP-1 receptor individually was assessed using molecular docking analyses. It revealed a higher affinity compared to the interaction of the individual GLP-1 and HSA-binding DARPin with the GLP-1 receptor and human serum albumin, respectively. The present study suggests that engineered fusion proteins can be used as a potential molecule in the treatment of type 2 diabetes, and this study provides insight into further experimental use of mimetic complexes as alternative molecules to be evaluated as new bio-breaks in the engineering of biological circuits in the treatment of type 2 diabetes.