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1.
Nature ; 633(8030): 646-653, 2024 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-39143220

RESUMO

Guanidine is a chemically stable nitrogen compound that is excreted in human urine and is widely used in manufacturing of plastics, as a flame retardant and as a component of propellants, and is well known as a protein denaturant in biochemistry1-3. Guanidine occurs widely in nature and is used by several microorganisms as a nitrogen source, but microorganisms growing on guanidine as the only substrate have not yet been identified. Here we show that the complete ammonia oxidizer (comammox) Nitrospira inopinata and probably most other comammox microorganisms can grow on guanidine as the sole source of energy, reductant and nitrogen. Proteomics, enzyme kinetics and the crystal structure of a N. inopinata guanidinase homologue demonstrated that it is a bona fide guanidinase. Incubation experiments with comammox-containing agricultural soil and wastewater treatment plant microbiomes suggested that guanidine serves as substrate for nitrification in the environment. The identification of guanidine as a growth substrate for comammox shows an unexpected niche of these globally important nitrifiers and offers opportunities for their isolation.


Assuntos
Amônia , Bactérias , Guanidina , Amônia/química , Amônia/metabolismo , Cristalografia por Raios X , Guanidina/metabolismo , Guanidina/química , Cinética , Microbiota , Modelos Moleculares , Nitrificação , Nitrogênio/metabolismo , Oxirredução , Proteômica , Microbiologia do Solo , Especificidade por Substrato , Águas Residuárias/microbiologia , Bactérias/enzimologia , Bactérias/crescimento & desenvolvimento , Bactérias/isolamento & purificação , Bactérias/metabolismo , Solo/química
2.
Mol Cell ; 74(5): 922-935.e6, 2019 06 06.
Artigo em Inglês | MEDLINE | ID: mdl-30979585

RESUMO

Enteropathogenic E. coli NleB and related type III effectors catalyze arginine GlcNAcylation of death domain (DD) proteins to block host defense, but the underlying mechanism is unknown. Here we solve crystal structures of NleB alone and in complex with FADD-DD, UDP, and Mn2+ as well as NleB-GlcNAcylated DDs of TRADD and RIPK1. NleB adopts a GT-A fold with a unique helix-pair insertion to hold FADD-DD; the interface contacts explain the selectivity of NleB for certain DDs. The acceptor arginine is fixed into a cleft, in which Glu253 serves as a base to activate the guanidinium. Analyses of the enzyme-substrate complex and the product structures reveal an inverting sugar-transfer reaction and a detailed catalytic mechanism. These structural insights are validated by mutagenesis analyses of NleB-mediated GlcNAcylation in vitro and its function in mouse infection. Our study builds a structural framework for understanding of NleB-catalyzed arginine GlcNAcylation of host death domain.


Assuntos
Escherichia coli Enteropatogênica/genética , Proteínas de Escherichia coli/química , Interações Hospedeiro-Patógeno/genética , Conformação Proteica , Fatores de Virulência/química , Animais , Apoptose/genética , Arginina/química , Arginina/genética , Coenzima A Ligases/química , Coenzima A Ligases/genética , Cristalografia por Raios X , Domínio de Morte/genética , Escherichia coli Enteropatogênica/patogenicidade , Proteínas de Escherichia coli/genética , Guanidina/química , Humanos , Manganês/química , Camundongos , Mutagênese , Proteína de Domínio de Morte Associada a Receptor de TNF/química , Proteína de Domínio de Morte Associada a Receptor de TNF/genética , Fatores de Virulência/genética
3.
Biochemistry ; 63(12): 1543-1552, 2024 Jun 18.
Artigo em Inglês | MEDLINE | ID: mdl-38787909

RESUMO

Hepatitis B virus (HBV) displays remarkable self-assembly capabilities that interest the scientific community and biotechnological industries as HBV is leading to an annual mortality of up to 1 million people worldwide (especially in Africa and Southeast Asia). When the ionic strength is increased, hepatitis B virus-like particles (VLPs) can assemble from dimers of the first 149 residues of the HBV capsid protein core assembly domain (Cp149). Using solution small-angle X-ray scattering, we investigated the disassembly of the VLPs by titrating guanidine hydrochloride (GuHCl). Measurements were performed with and without 1 M NaCl, added either before or after titrating GuHCl. Fitting the scattering curves to a linear combination of atomic models of Cp149 dimer (the subunit) and T = 3 and T = 4 icosahedral capsids revealed the mass fraction of the dimer in each structure in all the titration points. Based on the mass fractions, the variation in the dimer-dimer association standard free energy was calculated as a function of added GuHCl, showing a linear relation between the interaction strength and GuHCl concentration. Using the data, we estimated the energy barriers for assembly and disassembly and the critical nucleus size for all of the assembly reactions. Extrapolating the standard free energy to [GuHCl] = 0 showed an evident hysteresis in the assembly process, manifested by differences in the dimer-dimer association standard free energy obtained for the disassembly reactions compared with the equivalent assembly reactions. Similar hysteresis was observed in the energy barriers for assembly and disassembly and the critical nucleus size. The results suggest that above 1.5 M, GuHCl disassembled the capsids by attaching to the protein and adding steric repulsion, thereby weakening the hydrophobic attraction.


Assuntos
Capsídeo , Guanidina , Vírus da Hepatite B , Guanidina/química , Guanidina/farmacologia , Vírus da Hepatite B/química , Vírus da Hepatite B/fisiologia , Vírus da Hepatite B/efeitos dos fármacos , Capsídeo/química , Capsídeo/metabolismo , Proteínas do Capsídeo/química , Proteínas do Capsídeo/metabolismo , Espalhamento a Baixo Ângulo , Multimerização Proteica , Modelos Moleculares , Montagem de Vírus/efeitos dos fármacos , Difração de Raios X
4.
J Am Chem Soc ; 146(21): 14785-14798, 2024 May 29.
Artigo em Inglês | MEDLINE | ID: mdl-38743019

RESUMO

Selective RNA delivery is required for the broad implementation of RNA clinical applications, including prophylactic and therapeutic vaccinations, immunotherapies for cancer, and genome editing. Current polyanion delivery relies heavily on cationic amines, while cationic guanidinium systems have received limited attention due in part to their strong polyanion association, which impedes intracellular polyanion release. Here, we disclose a general solution to this problem in which cationic guanidinium groups are used to form stable RNA complexes upon formulation but at physiological pH undergo a novel charge-neutralization process, resulting in RNA release. This new delivery system consists of guanidinylated serinol moieties incorporated into a charge-altering releasable transporter (GSer-CARTs). Significantly, systematic variations in structure and formulation resulted in GSer-CARTs that exhibit highly selective mRNA delivery to the lung (∼97%) and spleen (∼98%) without targeting ligands. Illustrative of their breadth and translational potential, GSer-CARTs deliver circRNA, providing the basis for a cancer vaccination strategy, which in a murine model resulted in antigen-specific immune responses and effective suppression of established tumors.


Assuntos
Guanidina , RNA Mensageiro , Animais , Camundongos , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , RNA Mensageiro/química , Guanidina/química , Humanos , Serina/química
5.
Biochem Biophys Res Commun ; 715: 149994, 2024 Jun 30.
Artigo em Inglês | MEDLINE | ID: mdl-38692139

RESUMO

Many virus lysis/transport buffers used in molecular diagnostics, including the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA, contain guanidine-based chaotropic salts, primarily guanidine hydrochloride (GuHCl) or guanidine isothiocyanate (GITC). Although the virucidal effects of GuHCl and GITC alone against some enveloped viruses have been established, standardized data on their optimum virucidal concentrations against SARS-CoV-2 and effects on viral RNA stability are scarce. Thus, we aimed to determine the optimum virucidal concentrations of GuHCl and GITC against SARS-CoV-2 compared to influenza A virus (IAV), another enveloped respiratory virus. We also evaluated the effectiveness of viral RNA stabilization at the determined optimum virucidal concentrations under high-temperature conditions (35°C) using virus-specific real-time reverse transcription polymerase chain reaction. Both viruses were potently inactivated by 1.0 M GITC and 2.5 M GuHCl, but the GuHCl concentration for efficient SARS-CoV-2 inactivation was slightly higher than that for IAV inactivation. GITC showed better viral RNA stability than GuHCl at the optimum virucidal concentrations. An increased concentration of GuHCl or GITC increased viral RNA degradation at 35°C. Our findings highlight the need to standardize GuHCl and GITC concentrations in virus lysis/transport buffers and the potential application of these guanidine-based salts alone as virus inactivation solutions in SARS-CoV-2 and IAV molecular diagnostics.


Assuntos
Guanidina , Vírus da Influenza A , RNA Viral , SARS-CoV-2 , Manejo de Espécimes , SARS-CoV-2/efeitos dos fármacos , SARS-CoV-2/genética , Vírus da Influenza A/efeitos dos fármacos , Vírus da Influenza A/genética , Guanidina/farmacologia , Guanidina/química , RNA Viral/genética , Humanos , Manejo de Espécimes/métodos , Genoma Viral , COVID-19/virologia , COVID-19/diagnóstico , Chlorocebus aethiops , Células Vero , Inativação de Vírus/efeitos dos fármacos , Animais , Estabilidade de RNA/efeitos dos fármacos , Contenção de Riscos Biológicos , Guanidinas/farmacologia , Guanidinas/química , Sais/farmacologia , Sais/química
6.
Magn Reson Med ; 92(4): 1456-1470, 2024 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-38748853

RESUMO

PURPOSE: To develop a 3D, high-sensitivity CEST mapping technique based on the 3D stack-of-spirals (SOS) gradient echo readout, the proposed approach was compared with conventional acquisition techniques and evaluated for its efficacy in concurrently mapping of guanidino (Guan) and amide CEST in human brain at 3 T, leveraging the polynomial Lorentzian line-shape fitting (PLOF) method. METHODS: Saturation time and recovery delay were optimized to achieve maximum CEST time efficiency. The 3DSOS method was compared with segmented 3D EPI (3DEPI), turbo spin echo, and gradient- and spin-echo techniques. Image quality, temporal SNR (tSNR), and test-retest reliability were assessed. Maps of Guan and amide CEST derived from 3DSOS were demonstrated on a low-grade glioma patient. RESULTS: The optimized recovery delay/saturation time was determined to be 1.4/2 s for Guan and amide CEST. In addition to nearly doubling the slice number, the gradient echo techniques also outperformed spin echo sequences in tSNR: 3DEPI (193.8 ± 6.6), 3DSOS (173.9 ± 5.6), and GRASE (141.0 ± 2.7). 3DSOS, compared with 3DEPI, demonstrated comparable GuanCEST signal in gray matter (GM) (3DSOS: [2.14%-2.59%] vs. 3DEPI: [2.15%-2.61%]), and white matter (WM) (3DSOS: [1.49%-2.11%] vs. 3DEPI: [1.64%-2.09%]). 3DSOS also achieves significantly higher amideCEST in both GM (3DSOS: [2.29%-3.00%] vs. 3DEPI: [2.06%-2.92%]) and WM (3DSOS: [2.23%-2.66%] vs. 3DEPI: [1.95%-2.57%]). 3DSOS outperforms 3DEPI in terms of scan-rescan reliability (correlation coefficient: 3DSOS: 0.58-0.96 vs. 3DEPI: -0.02 to 0.75) and robustness to motion as well. CONCLUSION: The 3DSOS CEST technique shows promise for whole-cerebrum CEST imaging, offering uniform contrast and robustness against motion artifacts.


Assuntos
Amidas , Encéfalo , Imageamento Tridimensional , Imageamento por Ressonância Magnética , Humanos , Amidas/química , Imageamento Tridimensional/métodos , Imageamento por Ressonância Magnética/métodos , Encéfalo/diagnóstico por imagem , Reprodutibilidade dos Testes , Imagem Ecoplanar/métodos , Glioma/diagnóstico por imagem , Algoritmos , Razão Sinal-Ruído , Neoplasias Encefálicas/diagnóstico por imagem , Adulto , Processamento de Imagem Assistida por Computador/métodos , Masculino , Feminino , Guanidina/química
7.
Chemistry ; 30(30): e202401109, 2024 May 28.
Artigo em Inglês | MEDLINE | ID: mdl-38507249

RESUMO

A new class of superbasic, bifunctional peptidyl guanidine catalysts is presented, which enables the organocatalytic, atroposelective synthesis of axially chiral quinazolinediones. Computational modeling unveiled the conformational modulation of the catalyst by a novel phenyl urea N-cap, that preorganizes the structure into the active, folded state. A previously unanticipated noncovalent interaction involving a difluoroacetamide acting as a hybrid mono- or bidentate hydrogen bond donor emerged as a decisive control element inducing atroposelectivity. These discoveries spurred from a scaffold-oriented project inspired from a fascinating investigational BTK inhibitor featuring two stable chiral axes and relies on a mechanistic framework that was foreign to the extant lexicon of asymmetric catalysis.


Assuntos
Ligação de Hidrogênio , Conformação Molecular , Catálise , Estereoisomerismo , Quinazolinonas/química , Guanidina/química , Peptídeos/química , Modelos Moleculares , Tirosina Quinase da Agamaglobulinemia/antagonistas & inibidores , Tirosina Quinase da Agamaglobulinemia/química , Tirosina Quinase da Agamaglobulinemia/metabolismo
8.
Chemistry ; 30(26): e202304079, 2024 May 08.
Artigo em Inglês | MEDLINE | ID: mdl-38441909

RESUMO

The emerging role of Ribonucleic acids (RNAs) as therapeutics is alluring. However, RNAs are extremely labile under ambient conditions and typically need to be stored in cryogenic conditions (-20 °C to -80 °C). Hence, storage, stabilization, and transportation of RNA under ambient conditions have been an arduous task and remain an unsolved problem. In this work, a guanidinium-based ionic covalent organic framework (COF), TTGCl with nanotubular morphology, was synthesized and used as nano-reservoirs for room-temperature storage of RNA. To understand the role of the nanotubular morphology and chemical nature of TTGCl in stabilizing the RNA structure and for comparison purposes, a neutral COF, TMT-TT, is synthesized and studied. Further, density functional theory (DFT) studies confirmed non-covalent interaction between the COFs and the RNA nucleobases, facilitating reversible storage of RNA. RNA loaded in COFs was found to be resistant to enzymatic degradation when treated with RNase. Gel electrophoresis and sequencing confirmed the structural integrity of the recovered RNAs and their further processibility.


Assuntos
RNA , Temperatura , RNA/química , Estruturas Metalorgânicas/química , Guanidina/química , Conformação de Ácido Nucleico , Estabilidade de RNA , Teoria da Densidade Funcional
9.
Biomacromolecules ; 25(8): 5198-5211, 2024 Aug 12.
Artigo em Inglês | MEDLINE | ID: mdl-39073603

RESUMO

Monitoring membrane-mediated dialysis in real time with static and dynamic light scattering revealed distinctive differences, including reversibility/irreversibility, in the effects of ionic strength (NaCl) and the denaturant guanidine-HCl (Gd) on a synthetic polyelectrolyte and several types of biomacromolecules: protein, polysaccharide, and polyampholyte. Dialysis cycles against aqueous NaCl and Gd, and reverse back to the original aqueous solution, were monitored. The behavior of Na-polystyrenesulfonate was reversible and yielded a detailed polymer physics description. The biomacromolecules additionally showed hydrogen-bonding/hydrophobic (HP) interactions. An interpretive model was developed that considers the interplay among polyelectrolyte, polyampholyte, and HP potential energies in determining the different associative, aggregative, and dissociative behaviors. NaCl isolated purely electrostatic effects, whereas Gd combined electrostatic and HP effects. Some macromolecules showed partially reversible behavior, and others were completely irreversible. The dialysis monitoring method should prove useful for investigating fundamental macromolecular and colloid properties and for drug formulation and stability optimization.


Assuntos
Substâncias Macromoleculares , Concentração Osmolar , Substâncias Macromoleculares/química , Guanidina/química , Diálise/métodos , Ligação de Hidrogênio , Cloreto de Sódio/química , Interações Hidrofóbicas e Hidrofílicas , Polissacarídeos/química , Eletricidade Estática
10.
Biomacromolecules ; 25(8): 5149-5159, 2024 Aug 12.
Artigo em Inglês | MEDLINE | ID: mdl-39045816

RESUMO

As one of the gaseous signals in living cells, carbon monoxide (CO) not only participates in many biological activities but also serves as a therapeutic agent for the treatment of diseases. However, the limited applicability of CO in gas therapy emerges from the inconvenience of direct administration of CO. Here we reported the construction of guanidinylated CO-releasing micelles, which are composed of poly(trimethylene carbonate) (PTMC)-based CO donors. The in vitro studies demonstrated that micelles in the presence of light irradiation can induce cancer death, whereas no obvious toxicity to normal cells was observed. Moreover, the functionalization of guanidine groups imparts improved cellular uptake efficiency to micelles owing to the specific interactions with the surface of cells, which synergistically increase the anticancer capacity of the system. The guanidine-functionalized CO-releasing micelles provide a new strategy for the construction of CO-releasing nanocarriers, which are expected to find applications in gas therapeutics.


Assuntos
Monóxido de Carbono , Micelas , Cimento de Policarboxilato , Monóxido de Carbono/química , Humanos , Cimento de Policarboxilato/química , Guanidina/química , Portadores de Fármacos/química , Portadores de Fármacos/síntese química , Polímeros/química , Dioxanos/química
11.
J Org Chem ; 89(10): 6877-6891, 2024 May 17.
Artigo em Inglês | MEDLINE | ID: mdl-38662908

RESUMO

Anions have a profound effect on the properties of soluble proteins. Such Hofmeister effects have implications in biologics stability, protein aggregation, amyloidogenesis, and crystallization. However, the interplay between the important noncovalent interactions (NCIs) responsible for Hofmeister effects is poorly understood. To contribute to improving this state of affairs, we report on the NCIs between anions and ammonium and guanidinium hosts 1 and 2, and the consequences of these. Specifically, we investigate the properties of cavitands designed to mimic two prime residues for anion-protein NCIs─lysines and arginines─and the solubility consequences of complex formation. Thus, we report NMR and ITC affinity studies, X-ray analysis, MD simulations, and anion-induced critical precipitation concentrations. Our findings emphasize the multitude of NCIs that guanidiniums can form and how this repertoire qualitatively surpasses that of ammoniums. Additionally, our studies demonstrate the ease by which anions can dispense with a fraction of their hydration-shell waters, rearrange those that remain, and form direct NCIs with the hosts. This raises many questions concerning how solvent shell plasticity varies as a function of anion, how the energetics of this impact the different NCIs between anions and ammoniums/guanidiniums, and how this affects the aggregation of solutes at high anion concentrations.


Assuntos
Compostos de Amônio , Ânions , Arginina , Guanidina , Lisina , Guanidina/química , Ânions/química , Arginina/química , Compostos de Amônio/química , Lisina/química , Simulação de Dinâmica Molecular
12.
J Org Chem ; 89(9): 5977-5987, 2024 May 03.
Artigo em Inglês | MEDLINE | ID: mdl-38557022

RESUMO

Mellpaladines A-C (1-3) and dopargimine (4) are dopamine-derived guanidine alkaloids isolated from a specimen of Palauan Didemnidae tunicate as possible modulators of neuronal receptors. In this study, we isolated the dopargimine derivative 1-carboxydopargimine (5), three additional mellpaladines D-F (6-8), and serotodopalgimine (9), along with a dimer of serotonin, 5,5'-dihydroxy-4,4'-bistryptamine (10). The structures of these compounds were determined based on spectrometric and spectroscopic analyses. Compound 4 and its congeners dopargine (11), nordopargimine (15), and 2-(6,7-dimethoxy-3,4-dihydroisoquinolin-1-yl)ethan-1-amine (16) were synthetically prepared for biological evaluations. The biological activities of all isolated compounds were evaluated in comparison with those of 1-4 using a mouse behavioral assay upon intracerebroventricular injection, revealing key functional groups in the dopargimines and mellpaladines for in vivo behavioral toxicity. Interestingly, these alkaloids also emerged during a screen of our marine natural product library aimed at identifying antiviral activities against dengue virus, SARS-CoV-2, and vesicular stomatitis Indiana virus (VSV) pseudotyped with Ebola virus glycoprotein (VSV-ZGP).


Assuntos
Alcaloides , Dopamina , Urocordados , Animais , Alcaloides/química , Alcaloides/farmacologia , Alcaloides/isolamento & purificação , Alcaloides/síntese química , Urocordados/química , Camundongos , Dopamina/química , Dopamina/farmacologia , Estrutura Molecular , Guanidina/química , Guanidina/farmacologia , Antivirais/farmacologia , Antivirais/química , Antivirais/isolamento & purificação , Antivirais/síntese química , Guanidinas/química , Guanidinas/farmacologia , Guanidinas/isolamento & purificação , SARS-CoV-2/efeitos dos fármacos , Humanos
13.
J Nat Prod ; 87(4): 906-913, 2024 04 26.
Artigo em Inglês | MEDLINE | ID: mdl-38430199

RESUMO

The chemical diversity of annelids, particularly those belonging to the class Sipuncula, remains largely unexplored. However, as part of a Marine Biodiscovery program in Ireland, the peanut worm Phascolosoma granulatum emerged as a promising source of unique metabolites. The purification of the MeOH/CH2Cl2 extract of this species led to the isolation of six new linear guanidine amides, named phascolosomines A-F (1-6). NMR analysis allowed for the elucidation of their structures, all of which feature a terminal guanidine, central amide linkage, and a terminal isobutyl group. Notably, these guanidine amides were present in unusually high concentrations, comprising ∼3% of the dry mass of the organism. The primary concentration of the phascolosomines in the viscera is similar to that previously identified in linear amides from sipunculid worms and marine fireworms. The compounds from sipunculid worms have been hypothesized to be toxins, while those from fireworms are reported to be defensive irritants. However, screening of the newly isolated compounds for inhibitory bioactivity showed no significant inhibition in any of the assays conducted.


Assuntos
Amidas , Anelídeos , Guanidinas , Animais , Amidas/química , Amidas/farmacologia , Amidas/isolamento & purificação , Guanidina/química , Guanidina/farmacologia , Guanidinas/química , Guanidinas/farmacologia , Guanidinas/isolamento & purificação , Estrutura Molecular , Ressonância Magnética Nuclear Biomolecular , Anelídeos/química
14.
Bioorg Chem ; 147: 107410, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38688197

RESUMO

A new series of benzene-sulfonamide derivatives 3a-i was designed and synthesized via the reaction of N-(pyrimidin-2-yl)cyanamides 1a-i with sulfamethazine sodium salt 2 as dual Src/Abl inhibitors. Spectral data IR, 1H-, 13C- NMR and elemental analyses were used to confirm the structures of all the newly synthesized compounds 3a-i and 4a-i. Crucially, we screened all the synthesized compounds 3a-i against NCI 60 cancer cell lines. Among all, compound 3b was the most potent, with IC50 of 0.018 µM for normoxia, and 0.001 µM for hypoxia, compared to staurosporine against HL-60 leukemia cell line. To verify the selectivity of this derivative, it was assessed against a panel of tyrosine kinase EGFR, VEGFR-2, B-raf, ERK, CK1, p38-MAPK, Src and Abl enzymes. Results revealed that compound 3b can effectively and selectively inhibit Src/Abl with IC500.25 µM and Abl inhibitory activity with IC500.08 µM, respectively, and was found to be more potent on these enzymes than other kinases that showed the following results: EGFR IC500.31 µM, VEGFR-2 IC500.68 µM, B-raf IC500.33 µM, ERK IC501.41 µM, CK1 IC500.29 µM and p38-MAPK IC500.38 µM. Moreover, cell cycle analysis and apoptosis performed to compound 3b against HL-60 suggesting its antiproliferative activity through Src/Abl inhibition. Finally, molecular docking studies and physicochemical properties prediction for compounds 3b, 3c, and 3 h were carried out to investigate their biological activities and clarify their bioavailability.


Assuntos
Antineoplásicos , Proliferação de Células , Relação Dose-Resposta a Droga , Desenho de Fármacos , Ensaios de Seleção de Medicamentos Antitumorais , Inibidores de Proteínas Quinases , Proteínas Proto-Oncogênicas c-abl , Quinases da Família src , Humanos , Antineoplásicos/farmacologia , Antineoplásicos/síntese química , Antineoplásicos/química , Apoptose/efeitos dos fármacos , Proliferação de Células/efeitos dos fármacos , Guanidina/farmacologia , Guanidina/química , Guanidina/síntese química , Guanidina/análogos & derivados , Células HL-60 , Leucemia/tratamento farmacológico , Leucemia/patologia , Simulação de Acoplamento Molecular , Estrutura Molecular , Inibidores de Proteínas Quinases/farmacologia , Inibidores de Proteínas Quinases/síntese química , Inibidores de Proteínas Quinases/química , Proteínas Proto-Oncogênicas c-abl/antagonistas & inibidores , Proteínas Proto-Oncogênicas c-abl/metabolismo , Quinases da Família src/antagonistas & inibidores , Quinases da Família src/metabolismo , Relação Estrutura-Atividade , Cianamida/síntese química , Cianamida/química , Cianamida/farmacologia
15.
Nucleic Acids Res ; 50(10): 5401-5423, 2022 06 10.
Artigo em Inglês | MEDLINE | ID: mdl-35106589

RESUMO

Attaining sufficient tissue exposure at the site of action to achieve the desired pharmacodynamic effect on a target is an important determinant for any drug discovery program, and this can be particularly challenging for oligonucleotides in deep tissues of the CNS. Herein, we report the synthesis and impact of stereopure phosphoryl guanidine-containing backbone linkages (PN linkages) to oligonucleotides acting through an RNase H-mediated mechanism, using Malat1 and C9orf72 as benchmarks. We found that the incorporation of various types of PN linkages to a stereopure oligonucleotide backbone can increase potency of silencing in cultured neurons under free-uptake conditions 10-fold compared with similarly modified stereopure phosphorothioate (PS) and phosphodiester (PO)-based molecules. One of these backbone types, called PN-1, also yielded profound silencing benefits throughout the mouse brain and spinal cord at low doses, improving both the potency and durability of response, especially in difficult to reach brain tissues. Given these benefits in preclinical models, the incorporation of PN linkages into stereopure oligonucleotides with chimeric backbone modifications has the potential to render regions of the brain beyond the spinal cord more accessible to oligonucleotides and, consequently, may also expand the scope of neurological indications amenable to oligonucleotide therapeutics.


In this study, the authors explore the impact of nitrogen-containing (PN) backbones on oligonucleotides that promote RNase H-mediated degradation of a transcript in the central nervous system (CNS). Using Malat1, a ubiquitously expressed non-coding RNA that is predominately localized in the nucleus, and C9orf72, a challenging RNA target requiring a more nuanced targeting strategy, as benchmarks, they show that chimeric oligonucleotides containing stereopure PS and one of the more promising PN backbones (PN-1) have more potent and durable activity throughout the CNS compared with more traditional PS-modified molecules in mouse models. They demonstrate that potency and durability benefits in vivo derive at least in part from increased tissue exposure, especially in more difficult to reach regions of the brain. Ultimately, these benefits enabled the authors to demonstrate pharmacodynamic effects on Malat1 and C9orf72 RNAs in multiple brain regions with relatively low doses.


Assuntos
Oligonucleotídeos Antissenso , Animais , Células Cultivadas , Sistema Nervoso Central , Guanidina/química , Camundongos , Neurônios/efeitos dos fármacos , Oligonucleotídeos Antissenso/química , Oligonucleotídeos Antissenso/farmacologia , Oligonucleotídeos Fosforotioatos , Ribonuclease H/metabolismo
16.
Int J Mol Sci ; 25(10)2024 May 20.
Artigo em Inglês | MEDLINE | ID: mdl-38791607

RESUMO

This work investigated the cocatalytic activity of recently prepared guanidinium salts containing an oxanorbornane subunit in an (S)-proline-catalyzed aldol reaction. The activity was interpreted by the diastereoselectivity of the reaction (anti/syn ratio) and for the most interesting polycyclic guanidinium salt, the enantioselectivity of the reaction was determined. The results indicated a negative impact on the oxanorbornane unit if present as the flexible substituent. For most of the tested aldehydes, the best cocatalysts provided enantioselectivities above 90% and above 95% at room temperature and 0 °C, respectively, culminating in >99.5% for 4-chloro- and 2-nitrobenzaldehyde as the substrate. The barriers for forming four possible enantiomers were calculated and the results for two anti-enantiomers are qualitatively consistent with the experiment. Obtained results suggest that the representatives of furfurylguanidinium and rigid polycyclic oxanorbornane-substituted guanidinium salts are good lead structures for developing new cocatalysts by tuning the chemical space around the guanidine moiety.


Assuntos
Guanidinas , Prolina , Catálise , Prolina/química , Guanidinas/química , Estereoisomerismo , Aldeídos/química , Norbornanos/química , Guanidina/química , Estrutura Molecular
17.
Int J Mol Sci ; 25(17)2024 Aug 29.
Artigo em Inglês | MEDLINE | ID: mdl-39273310

RESUMO

By performing differential scanning calorimetry(DSC) measurements on RNase A, we studied the stabilization provided by the addition of potassium aspartate(KAsp) or potassium glutamate (KGlu) and found that it leads to a significant increase in the denaturation temperature of the protein. The stabilization proves to be mainly entropic in origin. A counteraction of the stabilization provided by KAsp or KGlu is obtained by adding common denaturants such as urea, guanidinium chloride, or guanidinium thiocyanate. A rationalization of the experimental data is devised on the basis of a theoretical approach developed by one of the authors. The main contribution to the conformational stability of globular proteins comes from the gain in translational entropy of water and co-solute ions and/or molecules for the decrease in solvent-excluded volume associated with polypeptide folding (i.e., there is a large decrease in solvent-accessible surface area). The magnitude of this entropic contribution increases with the number density and volume packing density of the solution. The two destabilizing contributions come from the conformational entropy of the chain, which should not depend significantly on the presence of co-solutes, and from the direct energetic interactions between co-solutes and the protein surface in both the native and denatured states. It is the magnitude of the latter that discriminates between stabilizing and destabilizing agents.


Assuntos
Ácido Aspártico , Ácido Glutâmico , Desnaturação Proteica , Ácido Aspártico/química , Desnaturação Proteica/efeitos dos fármacos , Ácido Glutâmico/química , Ribonuclease Pancreático/química , Ribonuclease Pancreático/metabolismo , Termodinâmica , Varredura Diferencial de Calorimetria , Entropia , Estabilidade Proteica , Guanidina/química , Guanidina/farmacologia , Ureia/química , Ureia/farmacologia , Conformação Proteica
18.
Biochemistry ; 62(11): 1643-1658, 2023 06 06.
Artigo em Inglês | MEDLINE | ID: mdl-37162303

RESUMO

The absorption and luminescence originating from protein charge transfer spectra (ProCharTS) depend on the proximity between multiple charged groups in a protein. This makes ProCharTS absorbance/luminescence intensity a sensitive probe for detecting changes in the protein structure, which alter the proximity among charged groups in the protein. In this work, ProCharTS absorbance of charge-rich proteins like human serum albumin (HSA), α3C, and α3W was used to monitor structural changes upon chemical denaturant-induced protein unfolding under equilibrium conditions. The denaturation midpoints were estimated using nonlinear regression analysis. For HSA, absorbance at 325 and 340 nm estimated the GdnHCl-induced denaturation midpoints to be 0.80 and 0.61 M, respectively. A similar analysis of α3C and α3W ProCharTS absorbance yielded denaturation midpoints of 0.88 and 0.86 M at 325 nm and 0.96 and 0.66 M at 340 nm, respectively. A previously reported molten globule-like state in the GdnHCl-induced HSA unfolding pathway was detected by the increase in HSA ProCharTS absorbance at 0.5 M GdnHCl. To validate the above results, protein unfolding was additionally monitored using conventional methods like circular dichroism (CD), Trp, and dansyl fluorescence. Our results suggest that disruption of charged amino acid sidechain contacts as revealed by ProCharTS occurs at lower denaturant concentrations compared to the loss of secondary/folded structure monitored by CD and fluorescence. Further, HSA ProCharTS absorbance at 315-340 nm revealed that tertiary contacts among charged residues were disrupted at lower GdnHCl concentrations compared to sequence adjacent contacts. Our data underscore the utility of ProCharTS as a novel label-free tool to track unfolding in charge-rich proteins.


Assuntos
Dobramento de Proteína , Humanos , Guanidina/química , Estrutura Secundária de Proteína , Desnaturação Proteica , Dicroísmo Circular , Espectrometria de Fluorescência
19.
J Comput Chem ; 44(3): 319-328, 2023 01 30.
Artigo em Inglês | MEDLINE | ID: mdl-35640228

RESUMO

Copper guanidine-quinoline complexes are an important class of bioinorganic complexes that find utilization in electron and atom transfer processes. By substitution of functional groups on the quinoline moiety the electron transfer abilities of these complexes can be tuned. In order to explore the full substitution space by simulations, the accurate theoretical description of the effect of functional groups is essential. In this study, we compare three different methods for the theoretical description of the structures. We use the semi-empirical tight-binding method GFN2-xTB, the density functional TPSSh and the double-hybrid functional B2PLYP. We evaluate the methods on five different complex pairs (Cu(I) and Cu(II) complexes), and compare how well calculated energies can predict the redox potentials. We find even though B2PLYP and TPSSh yield better accordance with the experimental structures. GFN2-xTB performs surprisingly well in the geometry optimization at a fraction of the computational cost. TPSSh offers a good compromise between computational cost and accuracy of the redox potential for real-life complexes.


Assuntos
Cobre , Quinolinas , Cobre/química , Guanidina/química , Modelos Moleculares , Benchmarking , Transporte de Elétrons , Quinolinas/química
20.
J Org Chem ; 88(16): 11694-11701, 2023 08 18.
Artigo em Inglês | MEDLINE | ID: mdl-37530571

RESUMO

Oxoanions such as carboxylates, phosphates, and sulfates play important roles in both chemistry and biology and are abundant on the cell surface. We report on the synthesis and properties of a rationally designed guanidinium-containing oxoanion binder, 1-guanidino-8-amino-2,7-diazacarbazole (GADAC). GADAC binds to a carboxylate, phosphate, and sulfate in pure water with affinities of 3.6 × 104, 1.1 × 103, and 4.2 × 103 M-1, respectively. Like 2-azacarbazole, which is a natural product that enables scorpions to fluoresce, GADAC is fluorescent in water (λabs = 356 nm, λem = 403 nm, ε = 13,400 M-1 cm-1). The quantum yield of GADAC is pH-sensitive, increasing from Φ = 0.12 at pH 7.4 to Φ = 0.53 at pH 4.0 as a result of the protonation of the aminopyridine moiety. The uptake of GADAC into live human melanoma cells is detectable in the DAPI channel at low micromolar concentrations. Its properties make GADAC a promising candidate for applications in oxoanion binding and fluorescence labeling in biological (e.g., the delivery of cargo into cells) and other contexts.


Assuntos
Fosfatos , Água , Humanos , Guanidina/química , Água/química , Ácidos Carboxílicos/química , Corantes
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