Structure-affinity Relationships Research Articles

Synthesis and structure-affinity relationships of spirocyclic σ1 receptor ligands with tetrahydropyran scaffold

The σ1 receptor plays a key role in the regulation of various processes in the human body; it is involved in the development of neurodegenerative and neuropsychiatric diseases and is overexpressed in several human tumors rendering it an important target for potential drug candidates. In this project, spirocyclic σ1 receptor ligands with different substituents in 4- and 9-position were synthesized and investigated for their σ1 receptor affinity and selectivity over related targets. The σ1 affinity of the ligands was correlated with their lipophilicity (logD7.4 value) giving insight into their lipophilic ligand efficiency (LLE). The (pyridin-3-yl)methyl derivative 5i showed a promising balance of high σ1 affinity (Ki(σ1) = 3.9 nM) and selectivity (> 250-fold) as well as high LLE of 5.8. 5i has a high plasma protein binding (89%) and promising metabolic stability in the presence of mouse liver microsomes and NADPH (83% intact after 90 min). Increasing the size of the piperidine ring of the spirocyclic ligands 5 to an azepane ring led to considerably increased σ1 affinity (Ki(5a) = 1.2 nM, Ki(23a) = 0.42 nM) and selectivity over σ2 receptors (5a: 45-fold, 23a: 150-fold).

Screening a knowledge-based library of low molecular weight compounds against the proline biosynthetic enzyme 1-pyrroline-5-carboxylate 1 (PYCR1).

Δ1-pyrroline-5-carboxylate reductase isoform 1 (PYCR1) is the last enzyme of proline biosynthesis and catalyzes the NAD(P)H-dependent reduction of Δ1-pyrroline-5-carboxylate to L-proline. High PYCR1 gene expression is observed in many cancers and linked to poor patient outcomes and tumor aggressiveness. The knockdown of the PYCR1 gene or the inhibition of PYCR1 enzyme has been shown to inhibit tumorigenesis in cancer cells and animal models of cancer, motivating inhibitor discovery. We screened a library of 71 low molecular weight compounds (average MW of 131 Da) against PYCR1 using an enzyme activity assay. Hit compounds were validated with X-ray crystallography and kinetic assays to determine affinity parameters. The library was counter-screened against human Δ1-pyrroline-5-carboxylate reductase isoform 3 and proline dehydrogenase (PRODH) to assess specificity/promiscuity. Twelve PYCR1 and one PRODH inhibitor crystal structures were determined. Three compounds inhibit PYCR1 with competitive inhibition parameter of 100 μM or lower. Among these, (S)-tetrahydro-2H-pyran-2-carboxylic acid (70 μM) has higher affinity than the current best tool compound N-formyl-l-proline, is 30 times more specific for PYCR1 over human Δ1-pyrroline-5-carboxylate reductase isoform 3, and negligibly inhibits PRODH. Structure-affinity relationships suggest that hydrogen bonding of the heteroatom of this compound is important for binding to PYCR1. The structures of PYCR1 and PRODH complexed with 1-hydroxyethane-1-sulfonate demonstrate that the sulfonate group is a suitable replacement for the carboxylate anchor. This result suggests that the exploration of carboxylic acid isosteres may be a promising strategy for discovering new classes of PYCR1 and PRODH inhibitors. The structure of PYCR1 complexed with l-pipecolate and NADH supports the hypothesis that PYCR1 has an alternative function in lysine metabolism.

Identification of ligands binding to MB327-PAM-1, a binding pocket relevant for resensitization of nAChRs

Desensitization of nicotinic acetylcholine receptors (nAChRs) can be induced by overstimulation with acetylcholine (ACh) caused by an insufficient degradation of ACh after poisoning with organophosphorus compounds (OPCs). Currently, there is no generally applicable treatment for OPC poisoning that directly targets the desensitized nAChR. The bispyridinium compound MB327, an allosteric modulator of nAChR, has been shown to act as a resensitizer of nAChRs, indicating that drugs binding directly to nAChRs can have beneficial effects after OPC poisoning. However, MB327 also acts as an inhibitor of nAChRs at higher concentrations and can thus not be used for OPC poisoning treatment. Consequently, novel, more potent resensitizers are required. To successfully design novel ligands, the knowledge of the binding site is of utmost importance. Recently, we performed in silico studies to identify a new potential binding site of MB327, MB327-PAM-1, for which a more affine ligand, UNC0646, has been described. In this work, we performed ligand-based screening approaches to identify novel analogs of UNC0646 to help further understand the structure-affinity relationship of this compound class. Furthermore, we used structure-based screenings and identified compounds representing four new chemotypes binding to MB327-PAM-1. One of these compounds, cycloguanil, is the active metabolite of the antimalaria drug proguanil and shows a higher affinity towards MB327-PAM-1 than MB327. Furthermore, cycloguanil can reestablish the muscle force in soman-inhibited rat muscles. These results can act as a starting point to develop more potent resensitizers of nAChR and to close the gap in the treatment after OPC poisoning.

Modular synthesis of dendritic ionic triphiles and their behavior in three-phase liquid–liquid–liquid system

Triphilic molecules possess unique features due to the presence of chemically distinct domains − oleophilic, hydrophilic, and fluorophilic. In bulk, they can form intriguing crystal structures, while in solutions, they can act as multi-purpose emulsifiers or form assemblies such as multi-compartment micelles applicable in drug delivery. However, their chemico-physical properties are still relatively unexplored. Namely, they have never been studied in a three-phase liquid–liquid–liquid system consisting of organic and fluorous solvents and water. Here we present an adaptive, modular synthesis of a novel type of dendritic ionic triphiles and a study of their solution behavior, with a focus on a three-phase toluene/water/perfluoro(methylcyclohexane) (PMC) system. The synthesis is based on the quaternization of various alkylimidazoles by a previously published type of carbosilane dendritic wedges bearing polyfluorinated chains of varied lengths at their periphery. This approach enables the facile combination of different organic and fluorous blocks and, thus, easy tailoring of final structures according to the results of this work. The distribution of triphiles in the selected three-phase system was mapped in a ternary diagram representing the mass proportions of individual domains. The distribution between toluene and PMC changes gradually depending on the sizes of the corresponding domains and significantly differs from the distribution in a biphasic system where water is absent (i.e., the fluorous partition coefficient). However, at a certain size of the fluorous domain, the molecules completely lose their affinity to the fluorous phase and gain affinity to water even though being still partially soluble in PMC. The results can help understand the structure-affinity relationship of triphilic compounds and can help find a substance with balanced affinities to all three solvents. Moreover, some of the prepared compounds manifested interesting surface activity, namely the emulsification capability on both phase interfaces or the formation of stable nanoparticles in an aqueous environment.

Structure-Affinity relationships of novel σ2R/TMEM97 ligands

The sigma 2 receptor (σ2R), which was recently identified as the transmembrane protein 97 (TMEM97), is increasingly attracting interest as a possible therapeutic target for indications in neuroscience. Toward identifying novel modulators of σ2R/TMEM97, we prepared a collection of benzoxazocine, benzomorphan, and methanobenzazepine ligands related to the known bioactive norbenzomorphans DKR-1677, FEM-1689, and EES-1686 and determined their Ki values for σ2R/TMEM97 and the sigma 1 receptor (σ1R). The σ2R/TMEM97 binding affinities and selectivities relative to σ1R of these new benzoxazocine, benzomorphan, and methanobenzazepine analogs are lower, often significantly lower, than their respective norbenzomorphan counterparts, suggesting the spatial orientation of pharmacophoric substituents is critical for binding to the two proteins. The benzoxazocine, benzomorphan, and methanobenzazepine congeners of DKR-1677 and FEM-1689 tend to be weakly selective for σ2R/TMEM97 versus σ1R, whereas EES-1686 derivatives exhibit the greatest selectivity, suggesting the size and/or nature of the substituent on the nitrogen atom of the scaffold may be important for selectivity. Computational docking studies were performed for the 1S,5R-and 1R,5S-enantiomers of DKR-1677, FEM-1689, and EES-1686 and their benzoxazocine, benzomorphan, and methanobenzazepine counterparts. These computations predict that the protonated amino group of each ligand forms a highly conserved salt bridge and a H-bonding interaction with Asp29 as well as a cation-π interaction with Tyr150 of σ2R/TMEM97. These electrostatic interactions are major driving forces for binding to σ2R/TMEM97 and are similar, though not identical, for each ligand. Other interactions within the well-defined binding pocket also tend to be comparable, but there are some major differences in how the hydrophobic aryl groups of various ligands interact with the protein surface external to the binding pocket. Overall, these studies show that the orientations of aryl and N-substituents on the norbenzomorphan and related scaffolds are important determinants of binding affinity of σ2R/TMEM97 ligands, and small changes can have significant effects upon binding profiles.

Topical drug delivery of licorice flavonoids and their structure-affinity relationship with the porcine skin

Traditional Chinese medicine (TCM) possesses a long history of clinical application in the transdermal prescriptions, however, their transdermal mechanisms had not been clearly elucidated ascribing to their complex ingredients and different content. In this work, we firstly provide insights reports on the transdermal mechanisms of licorice flavonoids (LFs) extracts and the structure-affinity relationship between LFs compounds and the skin. The permeation properties of LFs extracts were conducted on the porcine skin and rat skin. It was highlighted that chalones and flavanone molecules were easier to permeate through the skin from LFs extracts than isoflavone. Differ from other LFs compounds, insoluble licochalcone A and licoflavone A obtained a higher permeation amount from LFs extracts than its corresponding monomer ingredients affirmed through molecular dynamics simulation study. In the stratum corneum (SC), among 33 kinds of flavonoids, glabridin possessed the highest compatibility with the skin lipids. Furthermore, interaction parameters (χ) values between the drugs and ceramide were negatively correlated with the number of hydrogen bond donor (HBD), polarizability and polar surface area of LFs compounds. The HBD of LFs molecules could help drugs bind to the skin lipids and then formed appropriate hydrogen bond interactions with the skin lipids, further improving the affinity between the drugs and the skin. Moreover, LFs components permeated through the porcine skin by disturbing the lipids arrangement in the SC. In the epidermis and dermis, the positive number and absorption rate of LFs extracts by HaCaT cells was significantly higher than melanocytes and HSF cells after 6 h. This study provided a new approach to unveil the molecular mechanisms of LFs permeation, which gave a reference for permeation of other TCM extracts.

Coordination Chemistry of Sulfur-Containing Bifunctional Chelators: Toward in Vivo Stabilization of 64Cu PET Imaging Agents for Alzheimer's Disease.

The broader utilization of 64Cu positron emission tomography (PET) imaging agents has been hindered by the unproductive demetalation induced by bioreductants. To advance the development of 64Cu-based PET imaging tracers for Alzheimer's Disease (AD), there is a need for novel ligand design strategies. In this study, we developed sulfur-containing dithiapyridinophane (N2S2) bifunctional chelators (BFCs) as well as all nitrogen-based diazapyridinophane (N4) BFCs to compare their abilities to chelate Cu and target Aβ aggregates. Through spectrophotometric titrations and electrochemical measurements, we have demonstrated that the N2S2-based BFCs exhibit >10 orders of magnitude higher binding affinity toward Cu(I) compared to their N4-based counterparts, while both types of BFCs exhibit high stability constants toward Cu(II). Notably, solid state structures for both Cu(II) and Cu(I) complexes supported by the two ligand frameworks were obtained, providing molecular insights into their copper chelating abilities. Aβ binding experiments were conducted to study the structure-affinity relationship, and fluorescence microscopy imaging studies confirmed the selective labeling of the BFCs and their copper complexes. Furthermore, we investigated the potential of these ligands for the 64Cu-based PET imaging of AD through radiolabeling and autoradiography studies. We believe our findings provide molecular insights into the design of bifunctional Cu chelators that can effectively stabilize both Cu(II) and Cu(I) and, thus, can have significant implications for the development of 64Cu PET imaging as a diagnostic tool for AD.

In Silico Screening, In Vitro Mpro Inhibitory, and Adjunctive Therapy Value of Minocycline for the Treatment of COVID-19

What Is Known and Objective. Novel coronavirus disease (COVID-19) is still ravaging globally since its first discovery in 2019. With the continuous emergence of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) mutant strains, therapeutic entities are still needed to be discovered. This study was to explore SARS-CoV-2 inhibitors and therapeutic entities for COVID-19. Methods. Based on Lipinski’s rule of 5, a small-scale “old” drug database (clinical drugs being used in Ordos Central Hospital) was established, and in silico screening of Mpro inhibitors was conducted. Binding affinity and interaction as well as structure-affinity relationship were analyzed. Furthermore, molecular dynamic (MD) simulation of the selected drugs was performed to understand the conformational changes in docked complex. In vitro Mpro inhibition tests were performed according to established methods. Finally, literature review of potential “old” drug for the treatment of COVID-19 was conducted. Results and Discussion. The antibiotic minocycline, an inhibitor of bacterial ribosomal RNA, was screened out which showed the highest binding affinity (−9.6 kcal/mol). Beside the hydrogen bond with Cys145 and hydrophobic interactions, minocycline formed a pi-cation with His41, which strongly supported minocycline as a Michael addition acceptor to bind with the catalytic site of Mpro. MD simulation results show that minocycline displayed less conformational changes. The structure-affinity relationship was summarized based on minocycline analogs, and minocycline showed in vitro Mpro inhibitory activity with IC50 of 5 mM. More importantly, the literature review found that minocycline had both in vitro and in vivo broad-spectrum antiviral as well as anti-inflammatory activities, and the levels of a broad spectrum of biological markers during minocycline administration were opposed to those of COVID-19 conditions (both severe and nonsevere). What is New and Conclusion. Minocycline deserves an adjunctive therapeutic option for COVID-19 condition (both severe and nonsevere). This study shed a new light on drug-repurposing strategy for the viral disease.

Indazole as a Phenol Bioisostere: Structure-Affinity Relationships of GluN2B-Selective NMDA Receptor Antagonists.

Negative allosteric modulation of GluN2B subunit-containing NMDA receptors prevents overstimulation, resulting in neuroprotective effects. Since the phenol of prominent negative allosteric modulators is prone to rapid glucuronidation, its bioisosteric replacement by an indazole was envisaged. The key step in the synthesis was a Sonogashira reaction of non-protected iodoindazoles with propargylpiperidine derivatives. Modification of the alkynyl moiety allowed the introduction of several functional groups. The synthesized indazoles showed very high GluN2B affinity but limited selectivity over σ receptors. Molecular dynamics simulations revealed the same molecular interactions with the ifenprodil binding site as the analogous phenols. In two-electrode voltage-clamp experiments, enantiomeric 3-(4-benzylpiperidin-1-yl)-1-(1H-indazol-5-yl)propan-1-ols (S)-10a and (R)-10a displayed higher inhibitory activity than ifenprodil. In contrast to phenolic GluN2B antagonists, the indazoles were not conjugated with glucuronic acid. It can be concluded that the phenol of potent GluN2B antagonists can be replaced bioisosterically by an indazole, retaining the high GluN2B affinity and activity but inhibiting glucuronidation.

Structure-affinity relationships of stereoisomers of norbenzomorphan-derived σ2R/TMEM97 modulators

The sigma 2 receptor (σ2R), which is identical to transmembrane protein 97 (TMEM97), is attracting increasing interest as a possible therapeutic target for various indications in neuroscience. In continuation of a program to identify novel compounds that bind with high affinity and selectivity to σ2R/TMEM97, we performed structure-affinity-relationship (SAfiR) studies of several sets of σ2R/TMEM97 ligands having a B-norbenzomorphan ring core. Binding data for σ2R/TMEM97 and σ1R of several enantiomeric pairs of piperazine-substituted norbenzomorphans show the (1S,5R)-enantiomers have affinities (Ki = 9–75 nM) for σ2R/TMEM97 that are 2–3-fold higher than their enantiomorphic (1R,5S)-analogs; however, there is no clear trend for selectivity for σ2R/TMEM97 vs σ1R. A series of N-alkyl piperazino (1S,5R)-norbenzomorphans was then evaluated, and with the exception of compounds having N-alkyl groups substituted with oxygen or amino groups at C (2) of an ethylene chain, Ki values for σ2R/TMEM97 are less than 25 nM, and several compounds have good selectivities (ca 7–16-fold) for σ2R/TMEM97 vs σ1R. Mono-substituted carbobenzyloxy analogs have Ki values for σ2R/TMEM97 comparable to the unsubstituted parent (Ki = ca 7–27 nM), but replacing the N-acyloxy group with N-acyl or N-arylsulfonyl groups provides analogs having lower affinity and selectivity. Some congeners with bioisosteric replacements of the piperazine group on the (1S,5R)-norbenzomorphan core have high affinity (Ki = <30 nM) for σ2R/TMEM97, but selectivities are modest. Computational docking studies for racemic pairs of piperazino norbenzomorphans show that individual (1S,5R)- and (1R,5S)-enantiomers adopt distinct poses upon binding to σ2R/TMEM97, whereas ligands belongingto the same enantiomeric series adopt closely similar binding poses. The protonated amino group in each of the enantiomorphic ligands engages in highly conserved salt bridges with Asp29 and cation-π interactions with Tyr150 that are the primary determinants of binding affinity. There is no correlation between any of the computational parameter outputs and Ki values, but this is unsurprising given the small energetic differences involved. Modeling also suggest sthat some compounds can extend deeper into σ2R/TMEM97 binding pocket forming salt bridges with Glu73.

A fragment-based drug discovery developed on ciclopirox for inhibition of Hepatitis B virus core protein: An in silico study.

The Hepatitis B virus (HBV) core protein is an attractive target for preventing capsid assembly and viral replication. Drug repurposing strategies have introduced several drugs targeting HBV core protein. This study used a fragment-based drug discovery (FBDD) approach to reconstruct a repurposed core protein inhibitor to some novel antiviral derivatives. Auto Core Fragment in silico Screening (ACFIS) server was used for deconstruction-reconstruction of Ciclopirox in complex with HBV core protein. The Ciclopirox derivatives were ranked based on their free energy of binding (ΔGB). A quantitative structure affinity relationship (QSAR) was established on the Ciclopirox derivatives. The model was validated by a Ciclopirox-property-matched decoy set. A principal component analysis (PCA) was also assessed to define the relationship of the predictive variable of the QSAR model. 24-derivatives with a ΔGB (-16.56±1.46 Kcal.mol-1) more than Ciclopirox was highlighted. A QSAR model with a predictive power of 88.99% (F-statistics = 9025.78, corrected df(25), Pr > F = 0.0001) was developed by four predictive descriptors (ATS1p, nCs, Hy, F08[C-C]). The model validation showed no predictive power for the decoy set (Q2 = 0). No significant correlation was observed between predictors. By directly attaching to the core protein carboxyl-terminal domain, Ciclopirox derivatives may be able to suppress HBV virus assembly and subsequent viral replication inhibition. Hydrophobic residue Phe23 is a critical amino acid in the ligand binding domain. These ligands share the same physicochemical properties that lead to the development of a robust QSAR mode. The same strategy may also be used for future drug discovery of viral inhibitors.

Oligosaccharide Ligands of Galectin-4 and Its Subunits: Multivalency Scores Highly.

Galectins are carbohydrate-binding lectins that modulate the proliferation, apoptosis, adhesion, or migration of cells by cross-linking glycans on cell membranes or extracellular matrix components. Galectin-4 (Gal-4) is a tandem-repeat-type galectin expressed mainly in the epithelial cells of the gastrointestinal tract. It consists of an N- and a C-terminal carbohydrate-binding domain (CRD), each with distinct binding affinities, interconnected with a peptide linker. Compared to other more abundant galectins, the knowledge of the pathophysiology of Gal-4 is sparse. Its altered expression in tumor tissue is associated with, for example, colon, colorectal, and liver cancers, and it increases in tumor progression, and metastasis. There is also very limited information on the preferences of Gal-4 for its carbohydrate ligands, particularly with respect to Gal-4 subunits. Similarly, there is virtually no information on the interaction of Gal-4 with multivalent ligands. This work shows the expression and purification of Gal-4 and its subunits and presents a structure-affinity relationship study with a library of oligosaccharide ligands. Furthermore, the influence of multivalency is demonstrated in the interaction with a model lactosyl-decorated synthetic glycoconjugate. The present data may be used in biomedical research for the design of efficient ligands of Gal-4 with diagnostic or therapeutic potential.

A New Approach in Prebiotic Chemistry Studies: Proline Sorption Triggered by Mineral Surfaces Analysed Using XPS.

The role of minerals in the origin of life and prebiotic evolution remains unknown and controversial. Mineral surfaces have the potential to facilitate prebiotic polymerization due to their ability to adsorb and concentrate biomolecules that subsequently can catalyse reactions; however, the precise nature of the interaction between the mineral host and the guest biomolecule still needs to be understood. In this context, we spectroscopically characterized, using infrared, X-ray photoemission spectroscopy (XPS) and X-ray diffraction (XRD) techniques, the interaction between L-proline and montmorillonite, olivine, iron disulphide, and haematite (minerals of prebiotic interest), by evaluating their interaction from a liquid medium. This work provides insight into the chemical processes occurring between proline, the only cyclic amino acid, and this selection of minerals, each of them bearing a particular chemical and crystal structures. Proline was successfully adsorbed on montmorillonite, haematite, olivine, and iron disulphide in anionic and zwitterionic chemical forms, being the predominant form directly related to the mineral structure and composition. Silicates (montmorillonite) dominate adsorption, whereas iron oxides (haematite) show the lowest molecular affinity. This approach will help to understand structure-affinity relationship between the mineral surfaces and proline, one of the nine amino acids generated in the Miller-Urey experiment.

4'-OH as the Action Site of Lipids and MRP1 for Enhanced Transdermal Delivery of Flavonoids.

To date, the transdermal delivery study mainly focused on the drug delivery systems' design and efficacy evaluation. Few studies reported the structure-affinity relationship of the drug with the skin, further revealing the action sites of the drugs for enhanced permeation. Flavonoids attained a considerable interest in transdermal administration. The aim is to develop a systematic approach to evaluate the substructures that were favorable for flavonoid delivery into the skin and understand how these action sites interacted with lipids and bound to multidrug resistance protein 1 (MRP1) for enhanced transdermal delivery. First, we investigated the permeation properties of various flavonoids on the porcine skin or rat skin. We found that 4'-OH (hydroxyl group on the carbon 4' position) rather than 7-OH on the flavonoids was the key group for flavonoid permeation and retention, while 4'-OCH3 and -CH2═CH2-CH-(CH3)2 were unfavorable for drug delivery. 4'-OH could decrease flavonoids' lipophilicity to an appropriate log P and polarizability for better transdermal drug delivery. In the stratum corneum, flavonoids used 4'-OH as a hand to specifically grab the C═O group of the ceramide NS (Cer), which increased the miscibility of flavonoids and Cer and then disturbed the lipid arrangement of Cer, thereby facilitating their penetration. Subsequently, we constructed overexpressed MRP1 HaCaT/MRP1 cells by permanent transfection of human MRP1 cDNA in wild HaCaT cells. In the dermis, we observed that 4'-OH, 7-OH, and 6-OCH3 substructures were involved in H-bond formation within MRP1, which increased the flavonoid affinity with MRP1 and flavonoid efflux transport. Moreover, the expression of MRP1 was significantly enhanced after the treatment of flavonoids on the rat skin. Collectively, 4'-OH served as the action site for increased lipid disruption and enhanced affinity for MRP1, which facilitate the transdermal delivery of flavonoids, providing valuable guidelines for molecular modification and drug design of flavonoids.

Diastereoselective synthesis and structure-affinity relationships of σ1 receptor ligands with spirocyclic scaffold.

Spirocyclic scaffolds play an increasing role in drug discovery as they define a rigid three-dimensional space to increase specific interactions with protein binding sites. Herein, a spirocyclic center was introduced into the lead compound 1 to rigidify its flexible benzylaminoethyl side chain. The key step of the synthesis was the reaction of different α,β-unsaturated amides 6 and 13-16 with methyl acrylate in the presence of TBDMSOTf. DFT calculations explain the mechanism of this transformation as concerted Diels-Alder reaction (functionals B3LYP and TPSS) or double (aza)-Michael addition (functionals PBE and wB97X-D). After separation of the diastereomeric spirocyclic products 8 and 17-20, LiAlH4 reduction provided the spirocyclic hydroxymethyl piperidines 21a,b-25a,b showing low nanomolar σ1 affinity (Ki < 100 nM). trans-Configured ligands (a-series) showed higher or equal σ1 affinity and higher selectivity over σ2 receptors and GluN2B-NMDA receptors than their cis-configured analogs (b-series). The additional hydroxymethyl moiety brings the log D7.4 value in a promising range. The high σ1 affinity (Ki = 3.6 nM) and the low lipophilicity result in the highest lipophilic ligand efficiency for the dispiro compound 23a (LLE = 6.0). The spirocyclic compounds reported herein and in particular the dispiro compound 23a demonstrate that ligands containing a large number of sp3 C-atoms possess favorable pharmacological (σ1 receptor affinity, receptor selectivity) and physicochemical properties (log D7.4 value) resulting in promising LLE.

Screening of a Halogen-Enriched Fragment Library Leads to Unconventional Binding Modes.

We conceived the Halogen-Enriched Fragment Library (HEFLib) to investigate the potential of halogen bonds in the early stages of drug discovery. As the number of competitive interactions increases with ligand size, we reasoned that a binding mode relying on halogen bonding is more likely for fragments than highly decorated molecules. Thus, fragments could feature unexplored binding modes. We screened the HEFLib against the human kinase DYRK1a and verified micromolar binding fragments via isothermal titration calorimetry (ITC). The crystal structure of one fragment revealed a noncanonical binding mode, despite the fragment's classical hinge binding motif. In addition, the fragment occupies a secondary binding site. Both binding modes feature a halogen bond, which we evaluated by ab initio calculations. Structure-affinity relationship (SAR) from a set of analogues improves the affinity, provides a promising fragment-growth vector, and highlights the benefits and applicability of halogen bonds in early lead development.

Design and Screening of New Lead Compounds for Autism Based on QSAR Model and Molecular Docking Studies.

The purpose of the present study aims to develop a satisfactory model for predicting pro-social and pro-cognitive effects on azinesulfonamides of cyclic amine derivatives as potential antipsychotics. The three dimensional-quantitative structure affinity relationship (3D-QSAR) study was performed on a series of azinesulfonamides of cyclic amine derivative using comparative molecular similarity indices analysis (CoMSIA). The best statistical model of CoMSIA q2, r2, SEE and F values are 0.664, 0.973, 0.087, and 82.344, respectively. Based on the model contour maps and the highest activity structure of the 43rd compound, serial new structures were designed and the 43k1 compound was selected as the best structure. The dock results showed a good binding of 43k1 with the protein (PDB ID: 6A93). The QSAR model analysis of the contour maps can help us to provide guidelines for finding novel potential antipsychotics.

Interaction mechanism of benzophenone-type UV filters on bovine serum albumin: Insights from structure-affinity relationship

Benzophenone (BP)-type UV filters can cause structural changes of carrier protein in plasma. The binding process of five BP-type UV filters with bovine serum albumin (BSA) was investigated by multiple characterization methods, along with their structure-affinity relationship involving the structure of the five BP-type UV filters and their binding affinity for BSA. The BP-type UV filters investigated bound to BSA spontaneously, and altered conformation of BSA. The binding constants and number of binding sites between BP-type UV filters and BSA were 103–106 M−1 and 0.82–1.26, respectively. These BP-type UV filters and BSA interacted with the same binding forces and went through the similar binding process, suggesting that the benzophenone skeleton structure was primarily responsible for the BP-type UV filters and BSA binding, and changes in the structure of the BSA. The BP-type UV filters with hydroxyl substituent (BP-1 and BP-9) and non-polar molecules (BP-6) had a high affinity for binding BSA and had a greater impact on BSA conformation.

Interaction mechanism of flavonoids and Tartary buckwheat bran protein: A fluorescence spectroscopic and 3D-QSAR study

Tartary buckwheat bran protein (TBBP) is a valuable by-product of Tartary buckwheat processing. Current studies have indicated that TBBP is a desirable carrier and protector of flavonoids. However, the quantitative structure-affinity relationship of flavonoids with TBBP still remains to be elucidated. Here, by using the fluorescence spectroscopy method to measure the binding constants of 16 flavonoids with TBBP, we employ a combination of the atom-based three dimensional-quantitative structure-affinity relationships (3D-QSAR) and quantum-chemical calculation to explore the underlying binding mechanisms. We show that flavonoids can cause the intrinsic fluorescence quenching and form non-covalent complexes with TBBP driven by hydrogen bonding and van der Waal forces. The atom-based 3D-QSAR model reveals that the rutoside group at the C-7 position of flavones is favorable to enhance the binding constants of flavonoids with TBBP. Quantum-chemical calculations consistently disclose that the rutoside group can intensify interaction forces of flavonoids, thereby strengthening the binding. This work provides theoretical evidence that TBBP has the potential application to be raw materials for develop functional food, and be the delivery carriers of flavonoids.

Development of Bicyclo[3.1.0]hexane-Based A3 Receptor Ligands: Closing the Gaps in the Structure-Affinity Relationships.

The adenosine A3 receptor is a promising target for treating and diagnosing inflammation and cancer. In this paper, a series of bicyclo[3.1.0]hexane-based nucleosides was synthesized and evaluated for their P1 receptor affinities in radioligand binding studies. The study focused on modifications at 1-, 2-, and 6-positions of the purine ring and variations of the 5′-position at the bicyclo[3.1.0]hexane moiety, closing existing gaps in the structure–affinity relationships. The most potent derivative 30 displayed moderate A3AR affinity (Ki of 0.38 μM) and high A3R selectivity. A subset of compounds varied at 5′-position was further evaluated in functional P2Y1R assays, displaying no off-target activity.