Functionally important aromatic-aromatic and sulfur-π interactions in the D2 dopamine receptor

Role of CSF1R 550th-tryptophan in kusunokinin and CSF1R inhibitor binding and ligand-induced structural effect

Binding affinity is an important factor in drug design to improve drug-target selectivity and specificity. In this study, in silico techniques based on molecular docking followed by molecular dynamics (MD) simulations were utilized to identify the key residue(s) for CSF1R binding affinity among 14 pan-tyrosine kinase inhibitors and 15 CSF1R-specific inhibitors. We found tryptophan at position 550 (W550) on the CSF1R binding site interacted with the inhibitors' aromatic ring in a π-π way that made the ligands better at binding. Upon W550-Alanine substitution (W550A), the binding affinity of trans-(-)-kusunokinin and imatinib to CSF1R was significantly decreased. However, in terms of structural features, W550 did not significantly affect overall CSF1R structure, but provided destabilizing effect upon mutation. The W550A also did not either cause ligand to change its binding site or conformational changes due to ligand binding. As a result of our findings, the π-π interaction with W550's aromatic ring could be still the choice for increasing binding affinity to CSF1R. Nevertheless, our study showed that the increasing binding to W550 of the design ligand may not ensure CSF1R specificity and inhibition since W550-ligand bound state did not induce significantly conformational change into inactive state.

Catalyst-free decarboxylative cross-coupling of N-hydroxyphthalimide esters with tert-butyl 2-(trifluoromethyl)acrylate and its application

Here, we demonstrate a practical method toward the facile synthesis of CF3-containing amino acids through visible light promoted decarboxylative cross-coupling of a redox-active ester with tert-butyl 2-(trifluoromethyl)acrylate. The reaction was driven by the photochemical activity of electron donor-acceptor (EDA) complexes that were formed by the non-covalent interaction between a Hantzsch ester and a redox-active ester. The advantages of this protocol are its synthetic simplicity, rich functional group tolerance, and a cost-effective reaction system.

The C-terminus is essential for the stability of the mycobacterial channel protein MspA

Outer membrane proteins perform essential functions in uptake and secretion processes in bacteria. MspA is an octameric channel protein in the outer membrane of Mycobacterium smegmatis and is structurally distinct from any other known outer membrane protein. MspA is the founding member of a family with more than 3000 homologs and is one of the most widely used proteins in nanotechnological applications due to its advantageous pore structure and extraordinary stability. While a conserved C-terminal signal sequence is essential for folding and protein assembly in the outer membrane of Gram-negative bacteria, the molecular determinants of these processes are unknown for MspA. In this study, we show that mutation and deletion of methionine 183 in the highly conserved C-terminus of MspA and mutation of the conserved tryptophan 40 lead to a complete loss of protein in heat extracts of M. smegmatis. Swapping these residues partially restores the heat stability of MspA indicating that methionine 183 and tryptophan 40 form a conserved sulfur-π electron interaction, which stabilizes the MspA monomer. Flow cytometry showed that all MspA mutants are surface-accessible demonstrating that oligomerization and membrane integration in M. smegmatis are not affected. Thus, the conserved C-terminus of MspA is essential for its thermal stability, but it is not required for protein assembly in its native membrane, indicating that this process is mediated by a mechanism distinct from that in Gram-negative bacteria. These findings will benefit the rational design of MspA-like pores to tailor their properties in current and future applications.

Comparative homology of Pleurotus ostreatus laccase enzyme: Swiss model or Modeller?

Laccases stand out in the industrial context due to their versatile biotechnological applications. Although these enzymes are frequently investigated, currently, Pleurotus ostreatus laccase structural model is unknown. Therefore, this research aims to predict and validate a P. ostreatus laccase theoretical model by means of comparative homology. The laccase target's primary structure (AOM73725.1) was obtained from the NCBI database, the model was predicted from homologous structures obtained from the PDB (PDB-ID: 5A7E, 2HRG, 4JHU, 1GYC) using the Swiss-Model and Modeller, and was refined in GalaxyRefine. The models were validated using PROCHECK, VERIFY 3D, ERRAT, PROVE and QMEAN Z-score servers. Moreover, molecular docking between the laccase model (Lacc4MN) and ABTS was performed on AutoDock Vina. The models that were generated by the Modeller showed superior stereochemical and structural characteristics to those predicted by the Swiss Model. The refinement made it difficult to stabilize the copper atoms which are typical of laccases. The Lacc4MN model showed the interactions between the amino acids in the active site of the laccase and the copper atoms, thereby hinting the stabilization of the metal through electrostatic interactions with histidine and cysteine. The molecular docking between Lacc4MN and ABTS showed negative free energy and the formation of two hydrogen bonds involving the amino acids ASP 208 and GLY 268, and a Pi-sulfur bond between residue HIS 458 and ABTS, which demonstrates the typical catalytic functionality of laccases. Furthermore, the theoretical model Lacc4MN presented stereochemical and structural characteristics that allow its use in silico tests.Communicated by Ramaswamy H. Sarma.

Tinker, Tailor, Soldier, Spy: The Diverse Roles That Fluorine Can Play within Amino Acid Side Chains

Side chain-fluorinated amino acids are useful tools in medicinal chemistry and protein science. In this review, we outline some general strategies for incorporating fluorine atom(s) into amino acid side chains and for elaborating such building blocks into more complex fluorinated peptides and proteins. We then describe the diverse benefits that fluorine can offer when located within amino acid side chains, including enabling 19F NMR and 18F PET imaging applications, enhancing pharmacokinetic properties, controlling molecular conformation, and optimizing target-binding.

Enhanced π-π Stacking between Dipole-Bearing Single Molecules Revealed by Conductance Measurement

Dipoles are widely involved in π-π interactions and are central to many chemical and biological functions, but their influence on the strength of π-π interactions remains unclear. Here, we report a study of π-π interaction between azulene-based, polar single molecules and between naphthalene-based, nonpolar single molecules. By performing scanning tunneling microscopy break junction measurements of single-molecule conductance, we show that the π-stacked dimers formed by the azulene-based, polar aromatic structures feature higher electrical conductivity and mechanical stability than those formed by the naphthalene-based, nonpolar molecules. Mechanical control of π-π interactions in both rotational and translational motion reveals a sensitive dependence of the stacking strength on relative alignment between the dipoles. The antiparallel alignment of the dipoles was found to be the optimal stacking configuration that underpins the observed enhancement of π-π stacking between azulene-based single molecules. Density functional theory calculations further explained the observed enhancement of stacking strength and the corresponding charge transport efficiency. Our experimental and theoretical results show that the antiparallel alignment of the dipole moments significantly enhances the electronic coupling and mechanical stability of π-π stacking. In addition, in the formation of single-molecule junctions, the azulene group was experimentally and theoretically proved to form a Au-π contact with electrodes with high charge transport efficiency. This paper provides evidence and interpretation of the role of dipoles in π-π interactions at the single-molecule level and offers new insights into potential applications in supramolecular devices.

Tuning phenylalanine fluorination to assess aromatic contributions to protein function and stability in cells

The aromatic side-chains of phenylalanine, tyrosine, and tryptophan interact with their environments via both hydrophobic and electrostatic interactions. Determining the extent to which these contribute to protein function and stability is not possible with conventional mutagenesis. Serial fluorination of a given aromatic is a validated method in vitro and in silico to specifically alter electrostatic characteristics, but this approach is restricted to a select few experimental systems. Here, we report a group of pyrrolysine-based aminoacyl-tRNA synthetase/tRNA pairs (tRNA/RS pairs) that enable the site-specific encoding of a varied spectrum of fluorinated phenylalanine amino acids in E. coli and mammalian (HEK 293T) cells. By allowing the cross-kingdom expression of proteins bearing these unnatural amino acids at biochemical scale, these tools may potentially enable the study of biological mechanisms which utilize aromatic interactions in structural and cellular contexts.

Impacts of noncovalent interactions involving sulfur atoms on protein stability, structure, folding, and bioactivity

This review discusses the various types of noncovalent interactions in which sulfur atoms participate and their effects on protein stability, structure, folding and bioactivity. Current approaches and recommendations for modelling these noncovalent interactions (in terms of both geometries and interaction energies) are highlighted.

The Role of Tryptophan in π Interactions in Proteins: An Experimental Approach

In proteins, the amino acids Phe, Tyr, and especially Trp are frequently involved in π interactions such as π–π, cation−π, and CH−π bonds. These interactions are often crucial for protein structure and protein–ligand binding. A powerful means to study these interactions is progressive fluorination of these aromatic residues to modulate the electrostatic component of the interaction. However, to date no protein expression platform is available to produce milligram amounts of proteins labeled with such fluorinated amino acids. Here, we present a Lactococcus lactis Trp auxotroph-based expression system for efficient incorporation (≥95%) of mono-, di-, tri-, and tetrafluorinated, as well as a methylated Trp analog. As a model protein we have chosen LmrR, a dimeric multidrug transcriptional repressor protein from L. lactis. LmrR binds aromatic drugs, like daunomycin and riboflavin, between Trp96 and Trp96′ in the dimer interface. Progressive fluorination of Trp96 decreased the affinity for the drugs 6- to 70-fold, clearly establishing the importance of electrostatic π–π interactions for drug binding. Presteady state kinetic data of the LmrR–drug interaction support the enthalpic nature of the interaction, while high resolution crystal structures of the labeled protein–drug complexes provide for the first time a structural view of the progressive fluorination approach. The L. lactis expression system was also used to study the role of Trp68 in the binding of riboflavin by the membrane-bound riboflavin transport protein RibU from L. lactis. Progressive fluorination of Trp68 revealed a strong electrostatic component that contributed 15–20% to the total riboflavin-RibU binding energy.

Semi-Synthesis of N-Aryl Amide Analogs of Piperine from Piper nigrum and Evaluation of Their Antitrypanosomal, Antimalarial, and Anti-SARS-CoV-2 Main Protease Activities

Piper nigrum, or black pepper, produces piperine, an alkaloid that has diverse pharmacological activities. In this study, N-aryl amide piperine analogs were prepared by semi-synthesis involving the saponification of piperine (1) to yield piperic acid (2) followed by esterification to obtain compounds 3, 4, and 5. The compounds were examined for their antitrypanosomal, antimalarial, and anti-SARS-CoV-2 main protease activities. The new 2,5-dimethoxy-substituted phenyl piperamide 5 exhibited the most robust biological activities with no cytotoxicity against mammalian cell lines, Vero and Vero E6, as compared to the other compounds in this series. Its half-maximal inhibitory concentration (IC₅₀) for antitrypanosomal activity against Trypanosoma brucei rhodesiense was 15.46 ± 3.09 μM, and its antimalarial activity against the 3D7 strain of Plasmodium falciparum was 24.55 ± 1.91 μM, which were fourfold and fivefold more potent, respectively, than the activities of piperine. Interestingly, compound 5 inhibited the activity of 3C-like main protease (3CL^Pro) toward anti-SARS-CoV-2 activity at the IC₅₀ of 106.9 ± 1.2 μM, which was threefold more potent than the activity of rutin. Docking and molecular dynamic simulation indicated that the potential binding of 5 in the 3CL^pro active site had the improved binding interaction and stability. Therefore, new aryl amide analogs of piperine 5 should be investigated further as a promising anti-infective agent against human African trypanosomiasis, malaria, and COVID-19.

Novel Aurora A and Protein Kinase C (α, β1, β2, and θ) Multitarget Inhibitors: Impact of Selenium Atoms on the Potency and Selectivity

Aurora kinases and protein kinase C (PKC) have been shown to be involved in different aspects of cancer progression. To date, no dual Aurora/PKC inhibitor with clinical efficacy and low toxicity is available. Here, we report the identification of compound 2e as a potent small molecule capable of selectively inhibiting Aurora A kinase and PKC isoforms α, β1, β2 and θ. Compound 2e demonstrated significant inhibition of the colony forming ability of metastatic breast cancer cells in vitro and metastasis development in vivo. In vitro kinase screening and molecular modeling studies revealed the critical role of the selenium-containing side chains within 2e, where selenium atoms were shown to significantly improve its selectivity and potency by forming additional interactions and modulating the protein dynamics. In comparison to other H-bonding heteroatoms such as sulfur, our studies suggested that these selenium atoms also confer more favorable PK properties.

Comparative Analysis of Sulfonium-π, Ammonium-π, and Sulfur-π Interactions and Relevance to SAM-Dependent Methyltransferases

We report the measurement and analysis of sulfonium-π, thioether-π, and ammonium-π interactions in a β-hairpin peptide model system, coupled with computational investigation and PDB analysis. These studies indicated that the sulfonium-π interaction is the strongest and that polarizability contributes to the stronger interaction with sulfonium relative to ammonium. Computational studies demonstrate that differences in solvation of the trimethylsulfonium versus the trimethylammonium group also contribute to the stronger sulfonium-π interaction. In comparing sulfonium-π versus sulfur-π interactions in proteins, analysis of SAM- and SAH-bound enzymes in the PDB suggests that aromatic residues are enriched in close proximity to the sulfur of both SAM and SAH, but the populations of aromatic interactions of the two cofactors are not significantly different, with the exception of the Me-π interactions in SAM, which are the most prevalent interaction in SAM but are not possible for SAH. This suggests that the weaker interaction energies due to loss of the cation-π interaction in going from SAM to SAH may contribute to turnover of the cofactor.

Nickel-Catalyzed Cross-Coupling of Amino-Acid-Derived Alkylzinc Reagents with Alkyl Bromides/Chlorides: Access to Diverse Unnatural Amino Acids

Unnatural α-amino acids are important synthetic targets in the field of peptide science. Herein we report an efficient, versatile, and straightforward strategy for the synthesis of homophenylalanine derivatives via the nickel-catalyzed Csp3-Csp3 cross-coupling of (fluoro)benzyl bromides/chlorides with natural α-amino-acid-derived alkylzinc reagents. The current protocol features the advantages of a low-cost nickel catalyst system, synthetic convenience, and the tolerance of rich functionality and stereochemistry.

OUP accepted manuscript

Regulated transcription termination provides an efficient and responsive means to control gene expression. In bacteria, rho-independent termination occurs through the formation of an intrinsic RNA terminator loop, which disrupts the RNA polymerase elongation complex, resulting in its dissociation from the DNA template. Bacteria have a number of pathways for overriding termination, one of which is the formation of mutually exclusive RNA motifs. ANTAR domains are a class of antiterminator that bind and stabilize dual hexaloop RNA motifs within the nascent RNA chain to prevent terminator loop formation. We have determined the structures of the dimeric ANTAR domain protein EutV, from Enterococcus faecialis, in the absence of and in complex with the dual hexaloop RNA target. The structures illustrate conformational changes that occur upon RNA binding and reveal that the molecular interactions between the ANTAR domains and RNA are restricted to a single hexaloop of the motif. An ANTAR domain dimer must contact each hexaloop of the dual hexaloop motif individually to prevent termination in eubacteria. Our findings thereby redefine the minimal ANTAR domain binding motif to a single hexaloop and revise the current model for ANTAR-mediated antitermination. These insights will inform and facilitate the discovery of novel ANTAR domain RNA targets.

Discovery of a Potent Thieno[2,3-d]pyrimidine-2,4-dione-Based Protoporphyrinogen IX Oxidase Inhibitor through an In Silico Structure-Guided Optimization Approach

A key objective for herbicide research is to develop new compounds with improved bioactivity. Protoporphyrinogen IX oxidase (PPO) is an essential target for herbicide discovery. Here, we report using an in silico structure-guided optimization approach of our previous lead compound 1 and designed and synthesized a new series of compounds 2-6. Systematic bioassays led to the discovery of a highly potent compound 6g, 1-methyl-3-(2,2,7-trifluoro-3-oxo-4-(prop-2-yn-1-yl)-3,4-dihydro-2H-benzo[b][1,4]oxazin-6-yl)thieno[2,3-d]pyrimidine-2,4(1H,3H)-dione, which exhibited an excellent and wide spectrum of weed control at the rates of 30-75 g ai/ha by the postemergence application and is relatively safe on maize at 75 g ai/ha. Additionally, the K_i value of 6g to Nicotiana tabacum PPO (NtPPO) was found to be 2.5 nM, showing 3-, 12-, and 18-fold higher potency relative to compound 1 (K_i = 7.4 nM), trifludimoxazin (K_i = 31 nM), and flumioxazin (K_i = 46 nM), respectively. Furthermore, molecular simulations further suggested that the thieno[2,3-d]pyrimidine-2,4-dione moiety of 6g could form a more favorable π-π stacking interaction with the Phe392 of NtPPO than the heterocyclic moiety of compound 1. This study provides an effective strategy to obtain enzyme inhibitors with improved performance through molecular simulation and structure-guided optimization.

An "up" oriented methionine-aromatic structural motif in SUMO is critical for its stability and activity

Protein structural bioinformatic analyses suggest preferential associations between methionine and aromatic amino acid residues in proteins. Ab initio energy calculations highlight a conformation-dependent stabilizing interaction between the interacting sulfur-aromatic molecular pair. However, the relevance of buried methionine-aromatic motifs to protein folding and function is relatively unexplored. The Small Ubiquitin-Like Modifier (SUMO) is a β-grasp fold protein and a common posttranslational modifier that affects diverse cellular processes, including transcriptional regulation, chromatin remodeling, metabolic regulation, mitosis, and meiosis. SUMO is a member of the Ubiquitin-Like (UBL) protein family. Herein, we report that a highly conserved and buried methionine-phenylalanine motif is a unique signature of SUMO proteins but absent in other homologous UBL proteins. We also detect that a specific "up" conformation between the methionine-phenylalanine pair of interacting residues in SUMO is critical to its β-grasp fold. The noncovalent interactions of SUMO with its ligands are dependent on the methionine-phenylalanine pair. MD simulations, NMR, and biophysical and biochemical studies suggest that perturbation of the methionine-aromatic motif disrupts native contacts, modulates noncovalent interactions, and attenuates SUMOylation activity. Our results highlight the importance of conserved orientations of Met-aromatic structural motifs inside a protein core for its structure and function.

Contributions of methionine to recognition of trimethyllysine in aromatic cage of PHD domains: implications of polarizability, hydrophobicity, and charge on binding

Recognition of trimethyllysine (Kme3) by reader proteins is an important regulator of gene expression. This recognition event is mediated by an aromatic cage made up of 2-4 aromatic residues in the reader proteins that bind Kme3 via cation-π interactions. A small subset of reader proteins contain a methionine (Met) residue in place of an aromatic sidechain in the binding pocket. The unique role of sulfur in molecular recognition has been demonstrated in a number of noncovalent interactions recently, including interactions of thiols, thioethers, and sulfoxides with aromatic rings. However, the interaction of a thioether with an ammonium ion has not previously been investigated and the role of Met in binding Kme3 has not yet been explored. Herein, we systematically vary the Met in two reader proteins, DIDO1 and TAF3, and the ligand, Kme3 or its neutral analog tert-butyl norleucine (tBuNle), to determine the role of Met in the recognition of the cationic Kme3. Our studies demonstrate that Met contributes to binding via dispersion forces, with about an equal contribution to binding Kme3 and tBuNle, indicating that electrostatic interactions do not play a role. During the course of these studies, we also discovered that DIDO1 exhibits equivalent binding to tBuNle and Kme3 through a change in the mechanism of binding.

In silico investigation of potential inhibitors to main protease and spike protein of SARS-CoV-2 in propolis

Docking analysis of propolis's natural compound was successfully performed against SARS-CoV-2 main protease (Mpro) and spike protein subunit 2 (S2). Initially, the propolis's protein was screened using chromatography analysis and successfully identified 22 compounds in the propolis. Four compounds were further investigated, i.e., neoblavaisoflavone, methylophiopogonone A, 3'-Methoxydaidzin, and genistin. The binding affinity of 3'-Methoxydaidzin was -7.7 kcal/mol, which is similar to nelfinavir (control), while the others were -7.6 kcal/mol. However, we found the key residue of Glu A:166 in the methylophiopogonone A and genistin, even though the predicted binding energy slightly higher than nelfinavir. In contrast, the predicted binding affinity of neoblavaisoflavone, methylophiopogonone A, 3'-Methoxydaidzin, and genistin against S2 were -8.1, -8.2, -8.3, and -8.3 kcal/mol, respectively, which is far below of the control (pravastatin, -7.3 kcal/mol). Instead of conventional hydrogen bonding, the π bonding influenced the binding affinity against S2. The results reveal that this is the first report about methylophiopogonone A, 3'-Methoxydaidzin, and genistin as candidates for anti-viral agents. Those compounds can then be further explored and used as a parent backbone molecule to develop a new supplementation for preventing SARS-CoV-2 infections during COVID-19 outbreaks.

Virtual and experimental high throughput screening of substituted hydrazones on β-Tubulin polymerization

Microtubule targeting agents that disrupt the dynamic functioning of the mitotic spindle are some of the best chemotherapeutic agents. Interruption of microtubule dynamics through polymerization or depolymerization causes cell arrest leading to apoptosis. We report a novel class of aroylhydrazones with anticancer properties. Tubulin inhibition studies were performed using both computational and biological methods. Docking and pharmacophore mapping showed efficient binding between the ligands and the protein. Tubulin inhibition assay showed the aroylhydrazones to be inhibitors of tubulin polymerization. DFT studies explains the geometrical and electronic properties of the compounds. Furthermore, anticancer studies using lung and liver cancer cell lines gave low IC₅₀ values with the methyl substituted hydrazone MH-2 being the most potent. (IC₅₀ of 0.0896 and 0.1040 µM respectively). The methyl group is responsible for the effective binding to the protein. Thus, a new class of tubulin binding agents have been identified as potential agents in cancer therapy.

Dopamine D2 Receptor Agonist Binding Kinetics-Role of a Conserved Serine Residue

The forward (k_on) and reverse (k_off) rate constants of drug–target interactions have important implications for therapeutic efficacy. Hence, time-resolved assays capable of measuring these binding rate constants may be informative to drug discovery efforts. Here, we used an ion channel activation assay to estimate the k_ons and k_offs of four dopamine D₂ receptor (D₂R) agonists; dopamine (DA), p-tyramine, (R)- and (S)-5-OH-dipropylaminotetralin (DPAT). We further probed the role of the conserved serine S193^5.42 by mutagenesis, taking advantage of the preferential interaction of (S)-, but not (R)-5-OH-DPAT with this residue. Results suggested similar k_offs for the two 5-OH-DPAT enantiomers at wild-type (WT) D₂R, both being slower than the k_offs of DA and p-tyramine. Conversely, the k_on of (S)-5-OH-DPAT was estimated to be higher than that of (R)-5-OH-DPAT, in agreement with the higher potency of the (S)-enantiomer. Furthermore, S193^5.42A mutation lowered the k_on of (S)-5-OH-DPAT and reduced the potency difference between the two 5-OH-DPAT enantiomers. Kinetic K_ds derived from the k_off and k_on estimates correlated well with EC₅₀ values for all four compounds across four orders of magnitude, strengthening the notion that our assay captured meaningful information about binding kinetics. The approach presented here may thus prove valuable for characterizing D₂R agonist candidate drugs.

Highly Photostable and Luminescent Donor-Acceptor Molecules for Ultrasensitive Detection of Sulfur Mustard

Real-time, high signal intensity, and prolonged detection is challenging because of the rarity of fluorophores with both high photostability and luminescence efficiency. In this work, new donor-acceptor (D-A) molecules for overcoming these limitations are reported. A hybridized local and an intramolecular charge-transfer excited state is demonstrated to afford high photoluminescence efficiency of these D-A molecules in solution (≈100%). The twisted molecular structure and bulky alkyl chains effectively suppress π-π and dipole-dipole interactions, enabling high luminescence efficiency of 1 and 2 in the solid state (≈94% and 100%). Furthermore, two D-A aggregates exhibit high photostability as evidenced by 4% and 8% of the fluorescence decreasing after 6 h of continuous irradiation in air, which is in sharp contrast to ≈95% of fluorescence decreasing in a reference compound. Importantly, with these molecules, ultrasensitive detection of sulfur mustard (SM) with a record limit of 10 ppb and selective detection of SM in complex matrices are achieved.

FMODB: The World's First Database of Quantum Mechanical Calculations for Biomacromolecules Based on the Fragment Molecular Orbital Method

We developed the world's first web-based public database for the storage, management, and sharing of fragment molecular orbital (FMO) calculation data sets describing the complex interactions between biomacromolecules, named FMO Database (https://drugdesign.riken.jp/FMODB/). Each entry in the database contains relevant background information on how the data was compiled as well as the total energy of each molecular system and interfragment interaction energy (IFIE) and pair interaction energy decomposition analysis (PIEDA) values. Currently, the database contains more than 13 600 FMO calculation data sets, and a comprehensive search function implemented at the front-end. The procedure for selecting target proteins, preprocessing the experimental structures, construction of the database, and details of the database front-end were described. Then, we demonstrated a use of the FMODB by comparing IFIE value distributions of hydrogen bond, ion-pair, and XH/π interactions obtained by FMO method to those by molecular mechanics approach. From the comparison, the statistical analysis of the data provided standard reference values for the three types of interactions that will be useful for determining whether each interaction in a given system is relatively strong or weak compared to the interactions contained within the data in the FMODB. In the final part, we demonstrate the use of the database to examine the contribution of halogen atoms to the binding affinity between human cathepsin L and its inhibitors. We found that the electrostatic term derived by PIEDA greatly correlated with the binding affinities of the halogen containing cathepsin L inhibitors, indicating the importance of QM calculation for quantitative analysis of halogen interactions. Thus, the FMO calculation data in FMODB will be useful for conducting statistical analyses to drug discovery, for conducting molecular recognition studies in structural biology, and for other studies involving quantum mechanics-based interactions.

NTRK kinase domain mutations in cancer variably impact sensitivity to type I and type II inhibitors

Tyrosine kinase domains dynamically fluctuate between two main structural forms that are referred to as type I (DFG-in) or type II (DFG-out) conformations. Comprehensive data comparing type I and type II inhibitors are currently lacking for NTRK fusion-driven cancers. Here we used a type II NTRK inhibitor, altiratinib, as a model compound to investigate its inhibitory potential for larotrectinib (type I inhibitor)-resistant mutations in NTRK. Our study shows that a subset of larotrectinib-resistant NTRK1 mutations (V573M, F589L and G667C) retains sensitivity to altiratinib, while the NTRK1V573M and xDFG motif NTRK1G667C mutations are highly sensitive to type II inhibitors, including altiratinib, cabozantinib and foretinib. Moreover, molecular modeling suggests that the introduction of a sulfur moiety in the binding pocket, via methionine or cysteine substitutions, specifically renders the mutant kinase hypersensitive to type II inhibitors. Future precision treatment strategies may benefit from selective targeting of these kinase mutants based on our findings.

Deciphering the Unexpected Binding Capacity of the Third PDZ Domain of Whirlin to Various Cochlear Hair Cell Partners

Hearing is a mechanical and neurochemical process, which occurs in the hair cells of inner ear that converts the sound vibrations into electrical signals transmitted to the brain. The multi-PDZ scaffolding protein whirlin plays a critical role in the formation and function of stereocilia exposed at the surface of hair cells. In this article, we reported seven stereociliary proteins that encode PDZ binding motifs (PBM) and interact with whirlin PDZ3, where four of them are first reported. We solved the atomic resolution structures of complexes between whirlin PDZ3 and the PBMs of myosin 15a, CASK, harmonin a1 and taperin. Interestingly, the PBM of CASK and taperin are rare non-canonical PBM, which are not localized at the extreme C terminus. This large capacity to accommodate various partners could be related to the distinct functions of whirlin at different stages of the hair cell development.

In vitro exposure to ambient fine and ultrafine particles alters dopamine uptake and release, and D2 receptor affinity and signaling

The exposure to environmental pollutants, such as fine and ultrafine particles (FP and UFP), has been associated with increased risk for Parkinson's disease, depression and schizophrenia, disorders related to altered dopaminergic transmission. The striatum, a neuronal nucleus with extensive dopaminergic afferents, is a target site for particle toxicity, which results in oxidative stress, inflammation, astrocyte activation and modifications in dopamine content and D₂ receptor (D₂R) density. In this study we assessed the in vitro effect of the exposure to FP and UFP on dopaminergic transmission, by evaluating [³H]-dopamine uptake and release by rat striatal isolated nerve terminals (synaptosomes), as well as modifications in the affinity and signaling of native and cloned D₂Rs. FP and UFP collected from the air of Mexico City inhibited [³H]-dopamine uptake and increased depolarization-evoked [³H]-dopamine release in striatal synaptosomes. FP and UFP also enhanced D₂R affinity for dopamine in membranes from either rat striatum or CHO-K1 cells transfected with the long isoform of the human D₂R (hD_2LR)2LR). In CHO-K1-hD2L In CHO-K1-hD_2LR cells or striatal slices, FP and UFP increased the potency of dopamine or the D₂R agonist quinpirole, respectively, to inhibit forskolin-induced cAMP formation. The effects were concentration-dependent, with UFP being more potent than FP. These results indicate that FP and UFP directly affect dopaminergic transmission.

Shrinking of repeating unit length in leucine-rich repeats from double-stranded DNA viruses

Leucine-rich repeats (LRRs) are present in over 563,000 proteins from viruses to eukaryotes. LRRs repeat in tandem and have been classified into fifteen classes in which the repeat unit lengths range from 20 to 29 residues. Most LRR proteins are involved in protein-protein or ligand interactions. The amount of genome sequence data from viruses is increasing rapidly, and although viral LRR proteins have been identified, a comprehensive sequence analysis has not yet been done, and their structures, functions, and evolution are still unknown. In the present study, we characterized viral LRRs by sequence analysis and identified over 600 LRR proteins from 89 virus species. Most of these proteins were from double-stranded DNA (dsDNA) viruses, including nucleocytoplasmic large dsDNA viruses (NCLDVs). We found that the repeating unit lengths of 11 types are one to five residues shorter than those of the seven known corresponding LRR classes. The repeating units of six types are 19 residues long and are thus the shortest among all LRRs. In addition, two of the LRR types are unique and have not been observed in bacteria, archae or eukaryotes. Conserved strongly hydrophobic residues such as Leu, Val or Ile in the consensus sequences are replaced by Cys with high frequency. Phylogenetic analysis indicated that horizontal gene transfer of some viral LRR genes had occurred between the virus and its host. We suggest that the shortening might contribute to the survival strategy of viruses. The present findings provide a new perspective on the origin and evolution of LRRs.

The Prodigious Hydrogen Bonds with Sulfur and Selenium in Molecular Assemblies, Structural Biology, and Functional Materials

Hydrogen bonds (H-bonds) play important roles in imparting functionality to the basic molecules of life by stabilizing their structures and directing their interactions. Numerous studies have been devoted to understanding H-bonds involving highly electronegative atoms like nitrogen, oxygen, and halogens and consequences of those H-bonds in chemical reactions, catalysis, and structure and function of biomolecules; but the involvement of less electronegative atoms like sulfur and selenium in H-bond formation establishes the concept of noncanonical H-bonds. Initially belittled for the "weak" nature of their interactions, these perceptions have gradually evolved over time through dedicated efforts by several research groups. This has been facilitated by advancements in experimental methods for their detection through gas-phase laser spectroscopy and solution NMR spectroscopy, as well as through theoretical predictions from high level quantum chemical calculations.In this Account, we present insights into the versatility of the sulfur and selenium centered H-bonds (S/SeCHBs) by highlighting their multifarious applications in various fields from chemical reactions to optoelectronic properties to structural biology. Our group has highlighted the significance and strength of such H-bonds in natural and modified biomolecules. Here, we have reviewed several molecular assemblies, biomolecules, and functional materials, where the role of these H-bonds is pivotal in influencing biological functions. It is worth mentioning here that the precise experimental data obtained from gas-phase laser spectroscopy have contributed considerably to changing the existing perceptions toward S/SeCHBs. Thus, molecular beam experiments, though difficult to perform on smaller model thio- or seleno-substituted Molecules, etc. (amides, nucleobases, drug molecules), are inevitable to gather elementary knowledge and convincing concepts on S/SeCHBs that can be extended from a small four-atom sulfanyl dimer to a large 14 kDa iron-sulfur protein, ferredoxin. These H-bonds can also tailor a fascinating array of molecular frameworks and design supramolecular assemblies by inter- and intralinking of individual "molecular Lego-like" units.The discussion is indeed intriguing when it turns to the usage of S/SeCHBs in facile synthetic strategies like tuning regioselectivity in reactions, as well as invoking phenomena like dual phosphorescence and chemiluminescence. This is in addition to our investigations of the dispersive nature of the hydrogen bond between metal hydrides and sulfur or selenium as acceptor, which we anticipate would lead to progress in the areas of proton and hydride transfer, as well as force-field design. This Account demonstrates how ease of fabrication, enhanced efficiency, and alteration of physicochemical properties of several functional materials is facilitated owing to the presence of S/SeCHBs. Our efforts have been instrumental in the evaluation of various S/SeCHBs in flue gas capture, as well as design of organic energy harvesting materials, where dipole moment and polarizability have important roles to play. We hope this Account invokes newer perspectives with regard to how H-bonds with sulfur and selenium can be adequately adopted for crystal engineering, for more photo- and biophysical studies with different spectroscopic methods, and for developing next-generation field-effect transistors, batteries, superconductors, and organic thin-film transistors, among many other multifunctional materials for the future.

The functional role of the αM4 transmembrane helix in the muscle nicotinic acetylcholine receptor probed through mutagenesis and coevolutionary analyses

The activity of the muscle-type Torpedo nicotinic acetylcholine receptor (nAChR) is highly sensitive to lipids, but the underlying mechanisms remain poorly understood. The nAChR transmembrane α-helix, M4, is positioned at the perimeter of each subunit in direct contact with lipids and likely plays a central role in lipid sensing. To gain insight into the mechanisms underlying nAChR lipid sensing, we used homology modeling, coevolutionary analyses, site-directed mutagenesis, and electrophysiology to examine the role of the α-subunit M4 (αM4) in the function of the adult muscle nAChR. Ala substitutions for most αM4 residues, including those in clusters of polar residues at both the N and C termini, and deletion of up to 11 C-terminal residues had little impact on the agonist-induced response. Even Ala substitutions for coevolved pairs of residues at the interface between αM4 and the adjacent helices, αM1 and αM3, had little effect, although some impaired nAChR expression. On the other hand, Ala substitutions for Thr422 and Arg429 caused relatively large losses of function, suggesting functional roles for these specific residues. Ala substitutions for aromatic residues at the αM4-αM1/αM3 interface generally led to gains of function, as previously reported for the prokaryotic homolog, the Erwinia chrysanthemi ligand-gated ion channel (ELIC). The functional effects of individual Ala substitutions in αM4 were found to be additive, although not in a completely independent manner. Our results provide insight into the structural features of αM4 that are important. They also suggest how lipid-dependent changes in αM4 structure ultimately modify nAChR function.

A crosslinked, low pH-stable, mixed-mode cation-exchange like stationary phase made using the thiol-yne click reaction

Mixed-mode cation-exchange stationary phases are useful for the separation of mixtures containing hydrophobic, acidic, and basic molecules. To ensure that weak organic bases are protonated and carboxylic acids are neutral low pH mobile phases are required. Mixed-mode stationary phases that are stable at pH < 3 are needed. We synthesized a crosslinked structure along the surface of thiol functionalized silica gel particles using the thiol-yne click reaction. The alkyne, 1,7-octadiyne, was added to the 3-mercaptopropyl silica gel, then crosslinked using 1,6-hexanedithiol. Elemental analysis showed low octadiyne ligand surface coverage, but, stoichiometrically, three sulfurs were added to each octadiyne ligand during the crosslinking step, indicating that crosslinking occurred. The effect of the crosslinking on the stability was tested with a 50:50 (v/v) pH 0.50 5% TFA aqueous:acetonitrile mobile phase at 70 °C for six days, over 35,000 column volumes. The stationary phase showed good stability with the retention of triphenylene decreasing only 20% during that time. The Tanaka test showed that the phase has a methylene selectivity of 1.20 ± 0.04, a high shape selectivity of 2.71 ± 0.03, and a 3.98 ± 0.05 cation-exchange factor at pH 2.70. The phase has a selectivity factor for nitrobenzene and benzene of 1.41 ± 0.01, indicating the electron donating charge transfer characteristic of the phase. The mixed-mode characteristics of the phase were investigated using a mixture of the monoamine neurotransmitters norepinephrine, dopamine, and serotonin. Baseline resolution of the monoamines could be obtained using a simple 20 mM potassium phosphate (pH 2.70)/methanol mobile phase. Altering both the methanol content and the potassium ion concentration altered the retention of the monoamines indicating mixed-mode cation exchange characteristic of the crosslinked stationary phase.

Does Cysteine Rule (CysR) Complete the CendR Principle? Increase in Affinity of Peptide Ligands for NRP-1 Through the Presence of N-Terminal Cysteine

The structure-activity relationship of branched H-Lys(hArg)-Dab-Dhp-Arg-OH sequence analogues, modified with Cys-Asp or Cys at N-terminal amino acids (Lys, hArg), in VEGF-A₁₆₅/Neuropilin-1 complex inhibition is presented. The addition of Cys residue led to a 100-fold decrease in the IC₅₀ value, compared to the parent peptide. The change occurred regardless of coupling Cys to the free N-terminal amino group present in the main or the side chain. A few analogues extended by the attachment of Cys at the N-terminus of several potent NRP-1 peptide ligands documented in the literature are also presented. In all studied cases, the enhancement of inhibitory properties after the addition of Cys at the N-terminus is observed. It is particularly evident for the tetrapeptide derived from the C-terminus of VEGF-A₁₆₅ (KPRR), suggesting that extending the K/RXXK/R motif (CendR) with the Cys moiety can significantly improve affinity to NRP-1 of CendR peptides.

cis alkenes stabilized by intramolecular sulphurπ interactions

A series of alkenes with bistable isomers were obtained containing a thiophene/azoheteroaryl backbone. Visible light and heat-induced reversible cis ⇌ trans isomerizations were evidenced by UV-Vis and 1H NMR spectra. The stabilization of cis alkenes was attributed to intramolecular sulphurπ (Sπ) interactions, which were further supported by theoretical calculations.

Toward Understanding the Impact of Dimerization Interfaces in Angiotensin II Type 1 Receptor

Angiotensin II type 1 receptor (AT1R) is a prototypical class A G protein-coupled receptor (GPCR) that has an important role in cardiovascular pathologies and blood pressure regulation as well as in the central nervous system. GPCRs may exist and function as monomers; however, they can assemble to form higher order structures, and as a result of oligomerization, their function and signaling profiles can be altered. In the case of AT1R, the classical Gα_q/11 pathway is initiated with endogenous agonist angiotensin II binding. A variety of cardiovascular pathologies such as heart failure, diabetic nephropathy, atherosclerosis, and hypertension are associated with this pathway. Recent findings reveal that AT1R can form homodimers and activate the noncanonical (β-arrestin-mediated) pathway. Nevertheless, the exact dimerization interface and atomic details of AT1R homodimerization have not been still elucidated. Here, six different symmetrical dimer interfaces of AT1R are considered, and homodimers were constructed using other published GPCR crystal dimer interfaces as template structures. These AT1R homodimers were then inserted into the model membrane bilayers and subjected to all-atom molecular dynamics simulations. Our simulation results along with the principal component analysis and water pathway analysis suggest four different interfaces as the most plausible: symmetrical transmembrane (TM)1,2,8; TM5; TM4; and TM4,5 AT1R dimer interfaces that consist of one inactive and one active protomer. Moreover, we identified ILE238^6.33 as a hub residue in the stabilization of the inactive state of AT1R.

A comprehensive computational study of amino acid interactions in membrane proteins

Transmembrane proteins play a fundamental role in a wide series of biological processes but, despite their importance, they are less studied than globular proteins, essentially because their embedding in lipid membranes hampers their experimental characterization. In this paper, we improved our understanding of their structural stability through the development of new knowledge-based energy functions describing amino acid pair interactions that prevail in the transmembrane and extramembrane regions of membrane proteins. The comparison of these potentials and those derived from globular proteins yields an objective view of the relative strength of amino acid interactions in the different protein environments, and their role in protein stabilization. Separate potentials were also derived from α-helical and β-barrel transmembrane regions to investigate possible dissimilarities. We found that, in extramembrane regions, hydrophobic residues are less frequent but interactions between aromatic and aliphatic amino acids as well as aromatic-sulfur interactions contribute more to stability. In transmembrane regions, polar residues are less abundant but interactions between residues of equal or opposite charges or non-charged polar residues as well as anion-π interactions appear stronger. This shows indirectly the preference of the water and lipid molecules to interact with polar and hydrophobic residues, respectively. We applied these new energy functions to predict whether a residue is located in the trans- or extramembrane region, and obtained an AUC score of 83% in cross validation, which demonstrates their accuracy. As their application is, moreover, extremely fast, they are optimal instruments for membrane protein design and large-scale investigations of membrane protein stability.

Ultrasensitive Detection of Sulfur Mustard via Differential Noncovalent Interactions

In this work, we fabricate two types of hierarchical microspheres, i.e., one coassembled from two fluorene-based oligomers (1 and 2) and one self-assembled from a fluorene-based oligomer (1), for ultrasensitive and selective detection of trace sulfur mustard (SM) vapor. On the basis of distinct fluorescence responses of 1-2 coassembled and individual 1 hierarchical microspheres that originate from differential noncovalent interactions between analytes and these sensors, SM vapor can be ultrasensitively detected (30 ppb) and easily discriminated from various sulfides and other potential interferents. Our work that utilizes differential noncovalent interactions to give sensitive and selective fluorescence response patterns represents a new detection approach for SM and other hazardous chemicals.

Human mutations highlight an intersubunit cation-π bond that stabilizes the closed but not open or inactivated states of TRPV channels

An adequate response of a living cell to the ever-changing environment requires integration of numerous sensory inputs. In many cases, it can be achieved even at the level of a single receptor molecule. Polymodal transient receptor potential (TRP) channels have been shown to integrate mechanical, chemical, electric, and thermal stimuli. Inappropriate gating can lead to pathologies. Among the >60 known TRP vanilloid subfamily (V) 4 mutations that interfere with bone development are Y602C or R616Q at the S4-S5 linker. A cation-π bond between the conservative residues Y602 and R616 of neighboring subunits appears likely in many homologous channel structures in a closed state. Our experiments with TRPV4 mutants indicate that the resting-closed state remains stable while the bond is substituted by a salt bridge or disulfide bond, whereas disruption of the contact by mutations like Y602C or R616Q produces gain-of-function phenotypes when TRPV4 is heterologously expressed in the Xenopus oocyte or yeast. Our data indicate that the Y602-R616 cation-π interactions link the four S4-S5 linker helices together, forming a girdle backing the closed gate. Analogous cation-π bonds and the girdle are seen in many closed TRP channel structures. This girdle is not observed in the cryo-EM structure of amphibian TRPV4 (Protein Data Bank ID code 6BBJ), which appears to be in a different impermeable state-we hypothesize this is the inactivated state.

Synthesis and Evaluation of Oligomeric Thioether-Linked Carbacyclic β-(1→3)-Glucan Mimetics

Extrapolating from lessons learnt with previous low-molecular-weight β-(1→3)-glucan mimetics, we designed a series of minimal 2,4-dideoxy-thioether-linked carbacyclic β-(1→3)-glucan mimetics and synthesized di-, tri-, and tetramers in an enantiomerically pure form by an iterative sequence based on a simple building block readily available from commercial ( S)-(-)-3-cyclohexenecarboxylic acid. These substances were screened for their ability to inhibit anti-CR3-fluorescein isothiocyanate (FITC) staining of human neutrophils and anti-Dectin-1-FITC staining of mouse macrophages as well as for their ability to stimulate phagocytosis and pinocytosis. In each assay, the synthetic compounds displayed comparable activity to the corresponding native β-(1→3)-glucans, laminaritriose, and tetraose, suggesting that the exploitation of hydrophobic patches in the lectin-binding domains of CR3 and Dectin-1 is a promising strategy for the development of small-molecule analogues of β-(1→3)-glucans.

Discovery, cocrystallization and biological evaluation of novel piperidine derivatives as high affinity Ls-AChBP ligands possessing α7 nAChR activities

A series of novel pyridine-substituted piperidine derivatives were discovered as low nanomolar Ls-AChBP ligands with α7 nAChR partial agonism or antagonism activities. A high-resolution antagonist-bound Ls-AChBP complex was successfully resolved with a classic Loop C opening phenomenon and unique sulfur-π interactions which deviated from our previous docking mode to a large extent. With the knowledge of the co-complex, 27 novel piperidine derivatives were designed and synthesized. The structure-activity relationships (SARs) of the aromatic and pyridine regions were well established and binding modes were illustrated with the help of molecular docking which indicated that interactions with Trp 143 and the "water bridge" are essential for the high binding affinities. Halogen bonding as well as the space around 5'- or 6'- position of the pyridine ring was also proposed to influence the binding conformation of the compounds. Notably, two enantiomers of compound 2 showed opposite functions toward α7 nAChR and compound (S)-2 showed sub-nanomolar affinity (K_i = 0.86 nM) on Ls-AChBP and partial agonism (pEC₅₀ = 4.69 ± 0.11,Emax = 36.1%) on α7 nAChR with reasonable pharmacokinetics (PK) properties and fine ability of blood-brain-barrier (BBB) penetration. This study provided promising hits to develop candidates targeting nAChR-related CNS diseases.

Synthesis and Evaluation of 1,5-Dithia-d-laminaribiose, Triose, and Tetraose as Truncated β-(1→3)-Glucan Mimetics

The preparation and characterization of a series of di-, tri-, and tetrasaccharide analogues of β-(1→3)-glucans is described in which each pyranoside ring is replaced by a 5-thiopyranosyl ring and each glycosidic oxygen by a thioether. These oligomeric 1,5-dithio-d-glucopyranose derivatives were shown to inhibit the staining of human neutrophils and of mouse macrophages by fluorescent anti-CR3 and anti-Dectin-1 antibodies, respectively. The compounds were also demonstrated to stimulate phagocytosis and pinocytosis indicative of binding to the carbohydrate binding domains of complement receptor 3 (CR3) and Dectin-1. Activity in all three assays was optimum at the level of the trisaccharide mimic, suggesting that, while the replacement of ethereal oxygens by thioethers results in a greater affinity for the aromatic lined hydrophobic binding pockets, the presence of multiple longer C-S bonds eventually results in a mismatch and a loss of affinity.

Tipping the Balance between S-π and O-π Interactions

A comprehensive experimental survey consisting of 36 molecular balances was conducted to compare 18 pairs of S-π versus O-π interactions over a wide range of structural, geometric, and solvent parameters. A strong linear correlation was observed between the folding energies of the sulfur and oxygen balances across the entire library of balance pairs. The more stable interaction systematically switched from the O-π to S-π interaction. Computational studies of bimolecular PhSCH₃-arene and PhOCH₃-arene complexes were able to replicate the experimental trends in the molecular balances. The change in preference for the O-π to S-π interaction was due to the interplay of stabilizing (dispersion and solvophobic) and destabilizing (exchange-repulsion) terms arising from the differences in size and polarizability of the oxygen and sulfur atoms.

2-(4'-Pyridyl-N-oxide)-Substituted Hemithioindigos as Photoresponsive Guests for a Super Aryl-Extended Calix[4]pyrrole Receptor

We report the synthesis of two 2-(4'-pyridyl-N-oxide)-substituted hemithioindigos (HTIs). We probed their photoisomerization by using UV/Vis and ¹ H NMR spectroscopy techniques. Light irradiation at λ=450 nm provoked the isomerization of the HTI Z isomer to the E counterpart to a large extent (≈80 % at the photostationary state). ¹ H NMR titration experiments revealed the formation of thermodynamically and kinetically stable 1:1 inclusion complexes of the (Z)-HTI isomers with a super aryl-extended host (association constant>10⁴  m^-1 ). Photoirradiation at λ=450 nm of the inclusion complexes induced the isomerization of the bound HTI N-oxide to afford the (E)-HTI⊂calix[4]pyrrole complex. We determined accurate association constant values for the 1:1 inclusion complexes of the (Z)- and (E)-HTI isomers by using isothermal titration calorimetry experiments. The results showed that the stability constants of the (E)-HTI complexes were 2.2-2.8-fold lower than those of the (Z)-HTI counterparts, which explains the lack of light-induced release of the former to the bulk solution.

Probing the Inhibitor versus Chaperone Properties of sp²-Iminosugars towards Human β-Glucocerebrosidase: A Picomolar Chaperone for Gaucher Disease

A series of sp²-iminosugar glycomimetics differing in the reducing or nonreducing character, the configurational pattern (d-gluco or l-ido), the architecture of the glycone skeleton, and the nature of the nonglycone substituent has been synthesized and assayed for their inhibition properties towards commercial glycosidases. On the basis of their affinity and selectivity towards GH1 β-glucosidases, reducing and nonreducing bicyclic derivatives having a hydroxylation profile of structural complementarity with d-glucose and incorporating an N′-octyl-isourea or -isothiourea segment were selected for further evaluation of their inhibitory/chaperoning potential against human glucocerebrosidase (GCase). The 1-deoxynojirimycin (DNJ)-related nonreducing conjugates behaved as stronger GCase inhibitors than the reducing counterparts and exhibited potent chaperoning capabilities in Gaucher fibroblasts hosting the neuronopathic G188S/G183W mutation, the isothiourea derivative being indeed one of the most efficient chaperone candidates reported up to date (70% activity enhancement at 20 pM). At their optimal concentration, the four selected compounds promoted mutant GCase activity enhancements over 3-fold; yet, the inhibitor/chaperoning balance became unfavorable at much lower concentration for nonreducing as compared to reducing derivatives.

Sulfur(lone-pair)…π interactions with FAD in flavoenzymes

The interactions of π-systems with lone-pairs of electrons are known and have been described in biological systems, involving lone-pairs derived from metals, metalloids, sulfur, oxygen and nitrogen. This study describes a bibliographic survey of the disulfide-bound sulfur(lone-pair) interactions with π-systems residing in the flavin adenine dinucleotide (FAD) cofactor of oxidoreductase enzymes (flavoenzymes). Thus, of the 172 oxidoreductase enzymes evaluated for gamma-S(lone-pair)…π(FAD) interactions, 96 proteins (56%) exhibited these interactions corresponding; 61% of 350 the constituent monomers featured at least one gamma-S(lone-pair)…π(FAD) interaction. Two main points of association between the S(lone-pair) and the isoalloxazine moiety of FAD were identified, namely at the centroid of the bond linking the uracil and pyrazine rings (60%), and the centroid of the uracil ring (37%). Reflecting the nature of the secondary structure in three prominent classes of oxidoreductase enzymes: glutathione disulfide reductases (GR; 21 proteins), trypanothione disulfide reductases (TR, 14) and sulfhydryl oxidases (SOX, 22), the approach of the gamma-S(lone-pair) to the FAD residue was to the si-face of the isoalloxazine ring system, i.e. to the opposite side as the carbonyl residue, for all GR and TR examples, and to the re-face for all SOX examples. Finally, the attractive nature of the gamma-S(lone-pair)…π(FAD) interactions was confirmed qualitatively by an examination of the non-covalent interaction plots.

An allosteric link connecting the lipid-protein interface to the gating of the nicotinic acetylcholine receptor

The mechanisms underlying lipid-sensing by membrane proteins is of considerable biological importance. A unifying mechanistic question is how a change in structure at the lipid-protein interface is translated through the transmembrane domain to influence structures critical to protein function. Gating of the nicotinic acetylcholine receptor (nAChR) is sensitive to its lipid environment. To understand how changes at the lipid-protein interface influence gating, we examined how a mutation at position 418 on the lipid-facing surface of the outer most M4 transmembrane α-helix alters the energetic couplings between M4 and the remainder of the transmembrane domain. Human muscle nAChR is sensitive to mutations at position 418, with the Cys-to-Trp mutation resulting in a 16-fold potentiation in function that leads to a congenital myasthenic syndrome. Energetic coupling between M4 and the Cys-loop, a key structure implicated in gating, do not change with C418W. Instead, Trp418 and an adjacent residue couple energetically with residues on the M1 transmembrane α-helix, leading to a reorientation of M1 that stabilizes the open state. We thus identify an allosteric link connecting the lipid-protein interface of the nAChR to altered channel function.

Explaining urokinase type plasminogen activator inhibition by amino-5-hydroxybenzimidazole and two naphthamidine-based compounds through quantum biochemistry

Urokinase plasminogen activator (uPA) is a biomarker and therapeutic target for several cancer types whose inhibition has been shown to slow tumor growth and metastasis.