Engineering aptamers to enhance their interaction with protein target for selective inhibition of cell surface receptors.

Cell surface receptors play a key role in intracellular signaling, and their overexpression and activation are among the drivers of multiple diseases. Selective inhibition of cell surface receptors is important for regulating intracellular signaling pathways and cell behavior. Here, we design engineered aptamers to selectively inhibit receptor function. In this strategy, the aptamer specifically recognizing the extracellular structural domain of the EGFR, was conjugated to an adamantane moiety through linking arms of various lengths in order to obtain better performances toward EGFR. These interactions inhibit EGFR dimerization, thereby impeding the activation of downstream signaling pathways. It is shown that the adamantane-modified aptamers exhibit superior inhibition of downstream effector proteins relative to the unmodified aptamers. The optimal inhibitory effect was observed with a linker arm of 40 T-base in length. Notably, the best-performing adamantane-modified aptamer specifically binds to A549 cells with a dissociation constant (22.6 ± 4.5 nM) that is approximately 4-fold lower than that of the parent EGFR aptamer (94.4 ± 21.9 nM). We further combine the use of the adamantane-modified aptamer with that of genistein, a natural isoflavone compound with EGFR tyrosine kinase inhibition activity, to enhance the inhibitory effect on EGFR and its downstream signaling employing a synergistic action. This study is expected to provide a versatile approach for the improvement of existing aptamers obtaining increased selective inhibition of cell surface receptors.

Strain-Induced Structural Rearrangement Towards a White-Light-Emitting Adamantane-Type Cluster Dimer.

Group 14/16 adamantane-type hybrid clusters of the type [(RT)4E6] (T = group 14 element, E = group 16 element, R = organic group) have been reported to emit white-light when irradiated in an amorphous state with a continuous-wave (CW) infrared laser diode. This effect is enhanced if the cluster core is varied from a binary to a more complex composition. To further explore this phenomenon, we synthesized clusters with a multinary R/R'-T/T'-E/E' composition, including isolobal replacement of E with CH2, in [(2-NpSi){CH2Sn(S)Ph}3] (1, Np = naphthyl). When expanding one of the CH2 moieties to a C2H4 group, thus generating a R/R'-T/T'-E/E'/E'' cluster composition, we unexpectedly observed a dimerization of the initially formed, yet non-isolable adamantane-like cluster [(2-NpSi){CH2Sn(S)Ph}2{C2H4Sn(S)Ph}] (2) to [(2-NpSi){CH2Sn(S)Ph}2{C2H4Sn(S)Ph}]2 (3), exhibiting a heretofore unprecedented cluster architecture. Both monomeric 1 and dimeric 3, show white-light emission as thin films. The nonlinear optical response of the compounds was also modelled with DFT methods.

Preclinical Evaluation of Soluble Epoxide Hydrolase Inhibitor AMHDU against Neuropathic Pain.

Inhibition of soluble epoxide hydrolase (sEH) is a promising therapeutic strategy for treating neuropathic pain. These inhibitors effectively reduce diabetic neuropathic pain and inflammation induced by Freund's adjuvant which makes them a suitable alternative to traditional opioids. This study showcased the notable analgesic effects of compound AMHDU (1,1'-(hexane-1,6-diyl)bis(3-((adamantan-1-yl)methyl)urea)) in both inflammatory and diabetic neuropathy models. While lacking anti-inflammatory properties in a paw edema model, AMHDU is comparable to celecoxib as an analgesic in 30 mg/kg dose administrated by intraperitoneal injection. In a diabetic tactile allodynia model, AMHDU showed a prominent analgesic activity in 10 mg/kg intraperitoneal dose (p < 0.05). The effect is comparable to that of gabapentin, but without the risk of dependence due to a different mechanism of action. Low acute oral toxicity (>2000 mg/kg) and a high therapeutic index makes AMHDU a promising candidate for further structure optimization and preclinical evaluation.

Virtual screening, molecular docking, MD simulation studies, DFT calculations, ADMET, and drug likeness of Diaza-adamantane as potential MAPKERK inhibitors.

Introduction: Multiple sclerosis (MS) is an autoimmune and inflammatory disease that destroys the protective coating of central nervous system (CNS) nerve fibers and affects over 2.8 million people worldwide. Despite several studies on new therapeutic targets and lead compounds, MS disease has limited treatment options. This condition may be caused by a complicated interaction of environmental and genetic variables. Studies showed that MS-associated microglial cells' increased MAPKERK activity may cause CNS inflammation and oligodendrocyte damage. Thus, screening for lead compounds that inhibit MAPKERK may protect brain cells and slow disease progression. Methods: The study aims to discover compounds that may inhibit MAPKERK as a novel approach for protecting the nervous system in managing MS. The study includes in silico methods, such as virtual screening, molecular docking, Density-functional theory (DFT) investigations (using the B3LYP/6-31++G(d,p) basis set in a gas phase environment), drug likeness scores, and molecular dynamic (MD) simulations. Results and Discussion:During the docking process with the MAPKERK protein, it was shown that the ligand L12 receptor had the best binding affinity, with a docking score of -6.18 kcal/mol. To investigate the stability of the binding, a 100 ns MD simulation was performed on the complex formed by the MAPKERK protein and L12. The receptor-ligand combination exhibited significant stability throughout the duration of the MD simulation. Additionally, the pharmacokinetic and drug-likeness properties of these ligands suggest that they have the potential to be considered viable candidates for future development in MS management.

Amantadine mitigates the cytotoxic and genotoxic effects of doxorubicin in SH-SY5Y cells and reduces its mutagenicity.

Amantadine (AMA) is a useful drug in neuronal disorders, but few studies have been performed to access its toxicological profile. Conversely, doxorubicin (Dox) is a well-known antineoplastic drug that has shown neurotoxic effects leading to cognitive impairment. The aims of this study are to evaluate the cytotoxic, genotoxic, and mutagenic effects of AMA, as well as its possible protective actions against deleterious effects of Dox. The Salmonella/microsome assay was performed to assess mutagenicity while cytotoxicity and genotoxicity were evaluated in SH-SY5Y cells using MTT and comet assays. Possible modulating effects of AMA on the cytotoxicity, genotoxicity, and mutagenicity induced by Dox were evaluated through cotreatment procedures. Amantadine did not induce mutations in the Salmonella/microsome assay and decreased Dox-induced mutagenicity in the TA98 strain. AMA reduced cell viability and induced DNA damage in SH-SY5Y cells. In cotreatment with Dox, AMA attenuated the cytotoxicity of Dox and showed an antigenotoxic effect. In conclusion, AMA does not induce gene mutations, although it has shown a genotoxic effect. Furthermore, AMA decreases frameshift mutations induced by Dox as well as the cytotoxic and genotoxic effects of Dox in SH-SY5Y cells, suggesting that AMA can interfere with Dox mutagenic activity and attenuate its neurotoxic effects.

Asymmetric aza-Henry reaction toward trifluoromethyl ß-nitroamines and biological investigation of their adamantane-type derivatives.

Amino acid-derived quaternary ammonium salts were successfully applied in the asymmetric aza-Henry reaction of nitromethane to N-Boc trifluoromethyl ketimines. α-Trifluoromethyl ß-nitroamines were synthesized in good to excellent yields with moderate to good enantioselectivities. This reaction is distinguished by its mild conditions, low catalyst loading (1 mol%), and catalytic base. It also proceeded on a gram scale without loss of enantioselectivity. The products were transformed to a series of adamantane-type compounds containing chiral trifluoromethylamine fragments. The potent anticancer activities of these compounds against liver cancer HepG2 and melanoma B16F10 were evaluated. Six promising compounds with notable efficacy have potential for further development.

A Fluorinated Chaperone Gives X-ray Crystal Structures of Acyclic Natural Product Derivatives up to 338 Molecular Weight.

Crystallizing molecules with long flexible chains is a challenge, making it difficult to perform X-ray crystallography. Chaperones can assist in the crystallization of compounds that do not crystallize by themselves by producing solvate crystals that contain the analyte in their three-dimensional lattices. Among the most versatile chaperones for liquid analytes are tetraaryladamantanes (TAAs), but the size of the compounds that can be encapsulated is limited, and attempts to surpass this limit with known TAAs were unsuccessful. Here we report that 1,3,5,7-tetrakis(2-fluoro-4-methoxyphenyl)adamantane (TFM) is a crystallization chaperone for acyclic molecules up to the molecular weight of phytyl acetate (338 g/mol). Encapsulation of such a large acyclic compound was achieved when the analyte was esterified and when a two-step temperature protocol was used for crystallization. Exploratory work indicates that a drop to -20 °C allows for encapsulation of squalene (Mr 411 g/mol), albeit with positional disorder of the analyte. Our X-ray crystal structures of solvates with flexible analytes shed light on how crystalline order can be imposed on large acyclic analytes. The new, fluorinated TAA gives access to crystal structures that were inaccessible thus far.

Structure-Activity Relationships, Deuteration, and Fluorination of Synthetic Cannabinoid Receptor Agonists Related to AKB48, 5F-AKB-48, and AFUBIATA.

Synthetic cannabinoid receptor agonists (SCRAs) are a growing class of new psychoactive substances (NPS) commonly derived from an N-alkylated indole, indazole, or 7-azaindole scaffold. Diversification of this core (at the 3-position) with amide-linked pendant amino acid groups and modular N-alkylation (of the indole/indazole/7-azaindole core) ensures that novel SCRAs continue to enter the illicit drug market rapidly. In response to the large number of SCRAs that have been detected, pharmacological evaluation of this NPS class has become increasingly common. Adamantane-derived SCRAs have consistently appeared throughout the market since 2011, and as such, a systematic set of these derivatives was synthesized and pharmacologically evaluated. Deuterated and fluorinated adamantane derivatives were prepared to evaluate typical hydrogen bioisosteres, as well as evaluation of the newly detected AFUBIATA.

Design, synthesis, anti-infective potency and mechanism study of novel Ru-based complexes containing substituted adamantane as antibacterial agents.

Infections caused by Staphylococcus aureus (S. aureus) are increasing difficult to treat because this pathogen is easily resistant to antibiotics. However, the development of novel antibacterial agents with high antimicrobial activity and low frequency of resistance remains a huge challenge. Here, building on the coupling strategy, an adamantane moiety was linked to the membrane-active Ru-based structure and then developed three novel metalloantibiotics: [Ru(bpy)2(L)](PF6)2 (Ru1) (bpy = 2,2-bipyridine, L = amantadine modified ligand), [Ru(dmb)2(L)](PF6)2 (Ru2) (dmb = 4,4'-dimethyl-2,2'-bipyridine) and [Ru(dpa)2(L)](PF6)2 (Ru3), (dpa = 2,2'-dipyridylamine). Notably, complex Ru1 was identified to be the best candidate agent, showing greater efficacy against S. aureus than most of clinical antibiotics and low resistance frequencies. Mechanism studies demonstrated that Ru1 could not only increase the permeability of bacterial cell membrane and then caused the leakage of bacterial contents, but also promoted the production of reactive oxygen species (ROS) in bacteria. Importantly, complex Ru1 inhibited the biofilm formation, exotoxin secretion and increased the potency of some clinical used antibiotics. In addition, Ru1 showed low toxic in vivo and excellent anti-infective efficacy in two animal infection model. Thus, Ru-based metalloantibiotic bearing adamantane moiety are promising antibacterial agents, providing a certain research basis for the future antibiotics research.

A molecular docking exploration of the large extracellular loop of tetraspanin CD81 with small molecules.

Tetraspanin CD81 is a transmembrane protein used as a co-receptor by different viruses and implicated in some cancer and inflammatory diseases. The design of therapeutic small molecules targeting CD81 lags behind monoclonal antibodies and peptides but different synthetic and natural products binding to CD81 have been identified. We have investigated the interaction between synthetic compounds and CD81, considering both the cholesterol-bound full-length receptor and a truncated protein corresponding to the large extracellular loop (LEL) of the tetraspanin. They represent the closed and open conformations of the protein, respectively. Stable complexes were characterized with bi-aryl compounds (notably the quinolinone-benzothiazole 6) and atypical molecules bearing a 1-amino-boraadamantane scaffold well adapted to interact with CD81 (5a-d). In each case, the mode of binding to CD81 was analyzed, the binding sites identified and the molecular contacts determined. The narrow intra-LEL binding site of CD81 can accommodate the elongated bi-aryl 6 but not a series of isosteric compounds with a bis(bicyclic) scaffold. The bora-adamantane derivatives appeared to bind well to CD81, but essentially to the external surface of the protein loop. The binding selectivity of the compounds was assessed comparing binding to the LEL of tetraspanins CD81, CD9 and Tspan15. A net preference for CD81 over CD9 was evidenced, but the LEL of Tspan15 also provided a suitable binding site for the compounds, notably for the bora-adamantane derivatives. This work provides an aid to the identification and design of tetraspanin-binding small molecules, underlining the distinct behavior of the open and closed conformation of the protein for drug binding. Supplementary Information: The online version contains supplementary material available at 10.1007/s40203-024-00203-6.

Compounds based on Adamantyl-substituted Amino Acids and Peptides as Potential Antiviral Drugs Acting as Viroporin Inhibitors.

The discussion has revolved around the derivatives of amino acids and peptides containing carbocycles and their potential antiviral activity in vitro against influenza A, hepatitis C viruses, and coronavirus. Studies conducted on cell cultures reveal that aminoadamantane amino acid derivatives exhibit the capacity to hinder the replication of viruses containing viroporins. Furthermore, certain compounds demonstrate potent virucidal activity with respect to influenza A/H5N1 and hepatitis C virus particles. A conceptual framework for viroporin inhibitors has been introduced, incorporating carbocyclic motifs as membranotropic carriers in the structure, alongside a functional segment comprised of amino acids and peptides. These components correspond to the interaction with the inner surface of the channel's pore or another target protein.

Antibacterial Activity and Cytotoxicity Screening of Acyldepsipeptide-1 Analogues Conjugated to Silver/Indium/Sulphide Quantum Dots.

The continuous rise in bacterial infections and antibiotic resistance is the driving force behind the search for new antibacterial agents with novel modes of action. Antimicrobial peptides (AMPs) have recently gained attention as promising antibiotic agents with the potential to treat drug-resistant infections. Several AMPs have shown a lower propensity towards developing resistance compared to conventional antibiotics. However, these peptides, especially acyldepsipeptides (ADEPs) present with unfavorable pharmacokinetic properties, such as high toxicity and low bioavailability. Different ways to improve these peptides to be drug-like molecules have been explored, and these include using biocompatible nano-carriers. ADEP1 analogues (SC005-8) conjugated to gelatin-capped Silver/Indium/Sulfide (AgInS2) quantum dots (QDs) improved the antibacterial activity against Gram-negative (Escherichia coli and Pseudomonas aeruginosa), and Gram-positive (Bacillus subtilis, Staphylococcus aureus and Methicillin-resistant Staphylococcus aureus) bacteria. The ADEP1 analogues exhibited minimum inhibition concentrations (MIC) between 63 and 500 µM, and minimum bactericidal concentrations (MBC) values between 125 and 750 µM. The AgInS2-ADEP1 analogue conjugates showed enhanced antibacterial activity as evident from the MIC and MBC values, i.e., 1.6-25 µM and 6.3-100 µM, respectively. The AgInS2-ADEP1 analogue conjugates were non-toxic against HEK-293 cells at concentrations that showed antibacterial activity. The findings reported herein could be helpful in the development of antibacterial treatment strategies.

Discovery of adamantane-type polycyclic polyprenylated acylphloroglucinols that can prevent concanavalin A-induced autoimmune hepatitis in mice.

Hyperadamans A-G (1-7), seven new adamantane type polycyclic polyprenylated acylphloroglucinols (PPAPs), were isolated from Hypericum wilsonii N. Robson. Structurally, 1-4 were the first adamantanes bearing an unusual 2,7-dioxabicyclo-[2.2.1]-heptane fragment, and compound 5 was the first adamantane with a rare 1,6-dioxaspiro[4.4]nonane section. Importantly, 1-7 exhibited significant immunosuppressive activity on Con A-induced T-lymphocyte proliferation in vitro, with IC50 values ranging from 3.97 ± 0.10 to 18.12 ± 1.07 µM. Pretreatment with 1 in Con A-challenged autoimmune hepatitis mice could dramatically ameliorate the levels of hepatic injury indexes (ALT and AST) and reduce the product of proinflammatory cytokines (COX-2, IL-6, IL-1ß, IL-18, IL-23A and TNF-α). Furthermore, the protective effect of 1 on the Con A-induced liver injury was corroborated by the histological analysis and the immunohistochemistry.

Designing Organic π-Conjugated Molecules for Crystalline Solid Solutions: Adamantane-Substituted Naphthalenes.

We showcase herein organic crystalline solid solutions (CSSs) based on the simplest polycyclic aromatic hydrocarbon (PAH) scaffold, naphthalene, stabilized by dispersion forces induced by adamantane substitution. High thermal stability of the host and guest molecules synthesized by cross-coupling of dibromonaphthalene derivatives and 4-(1-adamantyl)phenyl boronic ester enabled formation of crystals by sublimation. We could generate binary monocrystalline solid solution systems proven by X-ray crystallography, the first system of designed CSSs stabilized exclusively via dispersion forces with structural evidence. These observations are additionally supported by lattice energy calculations and spectroscopic examinations. For the generation of CSSs, it is of utmost importance that the host and guest molecules have similar lattice energies and spatial compatibility. We anticipate that the thermostable organic CSS design demonstrated herein would be beneficial for functional materials and further investigation towards materials with unique properties.

Organic Polar Crystals, Second Harmonic Generation, and Piezoelectric Effects from Heteroadamantanes in the Space Group R3m.

Polar crystalline materials, a subset of the non-centrosymmetric materials, are highly sought after. Their symmetry properties make them pyroelectric and also piezoelectric and capable of second-harmonic generation (SHG). For SHG and piezoelectric applications, metal oxides are commonly used. The advantages of oxides are durability and hardness - downsides are the need for high-temperature synthesis/processing and often the need to include toxic metals. Organic polar crystals, on the other hand, can avoid toxic metals and can be amenable to solution-state processing. While the vast majority of polar organic molecules crystallize in non-polar space groups, we found that both 7-chloro-1,3,5-triazaadamantane, for short Cl-TAA, and also the related Br-TAA (but not I-TAA) form polar crystals in the space group R3m, easily obtained from dichloromethane solution. Measurements confirm piezoelectric and SHG properties for Cl-TAA and Br-TAA. When the two species are crystallized together, solid solutions form, suggesting that properties of future materials can be tuned continuously.

Narrowing Signal Distribution by Adamantane Derivatization for Amino Acid Identification Using an α-Hemolysin Nanopore.

The rapid progress in nanopore sensing has sparked interest in protein sequencing. Despite recent notable advancements in amino acid recognition using nanopores, chemical modifications usually employed in this process still need further refinements. One of the challenges is to enhance the chemical specificity to avoid downstream misidentification of amino acids. By employing adamantane to label proteinogenic amino acids, we developed an approach to fingerprint individual amino acids using the wild-type α-hemolysin nanopore. The unique structure of adamantane-labeled amino acids (ALAAs) improved the spatial resolution, resulting in distinctive current signals. Various nanopore parameters were explored using a machine-learning algorithm and achieved a validation accuracy of 81.3% for distinguishing nine selected amino acids. Our results not only advance the effort in single-molecule protein characterization using nanopores but also offer a potential platform for studying intrinsic and variant structures of individual molecules.

Do distributions of diamondoid hydrocarbons accumulated in oil-contaminated fish tissues help to identify the sources of oil?

Identifying the sources of environmental oil contamination can be challenging, especially for oil in motile organisms such as fish. Lipophilic hydrocarbons from oil can bioaccumulate in fish adipose tissue and potentially provide a forensic "fingerprint" of the original oil. Herein, diamondoid hydrocarbon distributions were employed to provide such fingerprints. Indices produced from diamondoids were used to compare extracts from fish adipose tissues and the crude and fuel oils to which the fish were exposed under laboratory conditions. A suite of 20 diamondoids was found to have bioaccumulated in the dietary-exposed fish. Cross-plots of indices between fish and exposure oils were close to the ideal 1:1 relationship. Comparisons with diamondoid distributions of non-exposure oils produced overall, but not exclusively, weaker correlations. Linear Discriminatory Analysis on a combined set of 15 diamondoid and bicyclane molecular ratios was able to identify the exposure oils, so a use of both compound classes is preferable.

Nascent pharmacological advancement in adamantane derivatives.

The adamantane moiety has attracted significant attention since its discovery in 1933 due to its remarkable structural, chemical, and medicinal properties. This molecule has a notable impact in the therapeutic field because of its "add-on" lipophilicity to any pharmacophoric moieties. As in the case of molecular hybridization, in which one pharmacophore is attached to another one(s) with a probability of increasing the biological activity, adding an adamantane unit improves the absorption distribution, metabolism and excretion properties of the resultant hybrid molecule. This review summarizes various reports highlighting the biological activities of adamantane-based synthetic compounds and their structure-activity relationship study. The information presented in this review may open up possible dimensions for adamantane-based drug development and discovery in the pharmaceutical industry after proper structural modifications.

Design, synthesis, and characterization of type I collagen mimetic peptides.

The current wound-healing collagen mimetic peptides (CMPs) have limitations such as poor membrane permeability and protease susceptibility. Herein, the solid-phase peptide synthesis of CMPs containing the integrin binding motif GFOGER is reported. The peptide sequences also consist of lipophilic moieties (adamantane and palmitic acid) for improved membrane permeability and different collagen-inducing tripeptides, namely, Thr-Thr-Lys (TTK), Gly-His-Lys (GHK), Gln-Pro-Arg (QPR), and Glu-Glu-Met (EEM). The synthesized peptides were successfully characterized and purified using liquid chromatography-mass spectrometry and preparative high-performance liquid chromatography techniques, respectively. The palmitic acid moiety increased the hydrophobic nature of the peptides, and they were retained longer on the stationary material of the reverse phase C-18 column. The three-dimensional parallel-strand helical structure of peptide DGD-GG-GFOGER-GG-TTK-palmitate was obtained using nuclear magnetic resonance spectroscopy and circular dichroism. The synthesized peptides have the desired helical structure, which can promote integrin binding.

Synthesis, characterization, molecular docking and molecular dynamics simulations of novel 2,5-disubstituted-1,3,4-thiadiazole derivatives as potential cholinesterase/monoamine oxidase dual inhibitors for Alzheimer's disease.

Designing multi-targeted drugs (MTD) for Alzheimer's disease (AD) is now one of the priorities for medicinal chemists, as the disease has a complicated not fully understood pathological nature and the approved mono-targeted drugs only alleviate the symptoms. In this study, the synthesis, spectral analyses and in vitro inhibition activity against cholinesterase (ChE) and monoamine oxidase (MAO) enzymes of a novel series of N-[5-(adamantan-1-yl)-1,3,4-thiadiazol-2-yl]-2-(4-un/substituted) cyclic secondary amino-acetamide/propanamide derivatives were done. Generally, derivatives were more selective against acetylcholinesterase (AChE) and h-MAO-B than butyrylcholinesterase (BChE) and h-MAO-A, respectively. Derivatives 4a, 4b, 3a, 3d and 3b ordered from the most potent to the least displayed significant inhibition against AChE. Also, derivatives 4a, 4b and 3a still maintained their significant inhibition against h-MAO-B in the same potency order, making them dual inhibitors and MTD candidates for AD. Binding interactions with several crucial amino acid residues for activity and selectivity as well as the stability of the most active derivatives-enzyme complex were confirmed utilizing molecular docking and molecular dynamic simulation studies.Communicated by Ramaswamy H. Sarma.

Novel 2,5-disubstituted-1,3,4-thiadiazole derivatives were synthesized.The ChEs/MAOs dual inhibition activity against Alzheimer's disease was tested.Compounds 4a, 4b and 3a were active dual inhibitor against both AChE and h-MAO-B.Compounds 3d and 3b were also active against AChE.No significant inhibition activity against BChE and h-MAO-A.