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1.
Chem Pharm Bull (Tokyo) ; 68(1): 58-63, 2020 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-31685780

RESUMO

Polycomb repressive complex 2 (PRC2) is an attractive drug target for anti-cancer treatment. Among the three core subunits (EZH2, EED and SUZ12) of PRC2, EZH2 is the catalytic subunit that methylates histone H3 lysine 27 (H3K27), while EED is the regulatory subunit. Besides the small-molecule inhibitors of EZH2, those targeting the protein-protein interaction (PPI) between EZH2 and EED have also been reported. Here, for the first time, we have identified the key residues that contributed most to the EED-EZH2 binding affinity by molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) calculations based on the 200 ns molecular dynamics simulation. Moreover, we report the identification of two novel and potent small-molecule inhibitors (35 and 49) of EZH2-EED interaction (bottom interaction surface) by virtual screening and biological evaluations. Binding modes of the two identified molecules with EED were probed by molecular docking. Additionally, 35 and 49 displayed cellular antiproliferative activity against diffuse large B-cell lymphoma (DLBCL) cancer cell line Toledo whose cell growth was driven by aberrant PRC2 activity. Our findings have provided structural insights for the design of novel EZH2-EED interaction inhibitors to regulate the activity of PRC2 complex.


Assuntos
Simulação de Acoplamento Molecular , Complexo Repressor Polycomb 2/metabolismo , Bibliotecas de Moléculas Pequenas/química , Sítios de Ligação , Ligação Competitiva , Domínio Catalítico , Linhagem Celular Tumoral , Proliferação de Células/efeitos dos fármacos , Desenho de Drogas , Humanos , Complexo Repressor Polycomb 2/antagonistas & inibidores , Complexo Repressor Polycomb 2/genética , Domínios e Motivos de Interação entre Proteínas/efeitos dos fármacos , Subunidades Proteicas/antagonistas & inibidores , Subunidades Proteicas/genética , Subunidades Proteicas/metabolismo , Proteínas Recombinantes/biossíntese , Proteínas Recombinantes/química , Proteínas Recombinantes/isolamento & purificação , Bibliotecas de Moléculas Pequenas/metabolismo , Bibliotecas de Moléculas Pequenas/farmacologia
2.
Chem Pharm Bull (Tokyo) ; 68(1): 64-69, 2020 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-31708557

RESUMO

Invasive fungal disease constitutes a growing health problem and development of novel antifungal drugs with high potency and selectivity are in an urgent need. In this study, a novel series of triazole derivatives containing different ester skeleton were designed and synthesized. Microdilution broth method was used to investigate antifungal activity. Significant inhibitory activity of compounds 5c, 5d, 5e, 5f, 5m and 5n was evaluated against the Candida albicans (I), Candida albicans clinical isolate (II), Candida glabrata clinical isolate (I), and Candida glabrata (II) with minimum inhibitory concentrations (MIC80) values ranging from 2 to 16 µg/mL. Notably, compounds 5e and 5n showed the best inhibition against Candida albicans (II), Candida glabrata (I), and Candida glabrata (II) at the concentrations of 2 and 8 µg/mL, respectively. Molecular docking study revealed that the target compounds interacted with CYP51 mainly through hydrophobic and van der Waals interactions. The results indicated that these novel triazole derivatives could serve as promising leads for development of antifungal agents.


Assuntos
Antifúngicos/síntese química , Desenho de Drogas , Simulação de Acoplamento Molecular , Triazóis/química , Antifúngicos/química , Antifúngicos/farmacologia , Sítios de Ligação , Candida/efeitos dos fármacos , Domínio Catalítico , Ésteres/química , Testes de Sensibilidade Microbiana , Eletricidade Estática , Esterol 14-Desmetilase/química , Esterol 14-Desmetilase/metabolismo , Relação Estrutura-Atividade , Triazóis/síntese química , Triazóis/farmacologia
3.
Chemistry ; 26(1): 148-154, 2020 Jan 02.
Artigo em Inglês | MEDLINE | ID: mdl-31503360

RESUMO

We present a new approach for the identification of inhibitors of phosphorylation-dependent protein-protein interaction domains, in which phenolic fragments are adapted by in silico O-phosphorylation before docking-based screening. From a database of 10 369 180 compounds, we identified 85 021 natural product-derived phenolic fragments, which were virtually O-phosphorylated and screened for in silico binding to the STAT3 SH2 domain. Nine screening hits were then synthesized, eight of which showed a degree of in vitro inhibition of STAT3. After analysis of its selectivity profile, the most potent inhibitor was then developed to Stafia-1, the first small molecule shown to preferentially inhibit the STAT family member STAT5a over the close homologue STAT5b. A phosphonate prodrug based on Stafia-1 inhibited STAT5a with selectivity over STAT5b in human leukemia cells, providing the first demonstration of selective in vitro and intracellular inhibition of STAT5a by a small-molecule inhibitor.


Assuntos
Organofosfonatos/química , Fator de Transcrição STAT5/antagonistas & inibidores , Proteínas Supressoras de Tumor/antagonistas & inibidores , Sítios de Ligação , Produtos Biológicos/química , Linhagem Celular Tumoral , Sobrevivência Celular/efeitos dos fármacos , Humanos , Simulação de Acoplamento Molecular , Organofosfonatos/metabolismo , Organofosfonatos/farmacologia , Fosforilação , Pró-Fármacos/química , Pró-Fármacos/metabolismo , Fator de Transcrição STAT5/metabolismo , Relação Estrutura-Atividade , Proteínas Supressoras de Tumor/metabolismo , Domínios de Homologia de src
4.
Chemistry ; 26(1): 49-88, 2020 Jan 02.
Artigo em Inglês | MEDLINE | ID: mdl-31483909

RESUMO

Drugs in the chemical space beyond the rule of 5 (bRo5) can modulate targets with difficult binding sites while retaining cell permeability and oral absorption. Reviewing the syntheses of bRo5 drugs approved since 1990 highlights synthetic chemistry's contribution to drug discovery in this space. Initially, bRo5 drugs were mainly natural products and semi-synthetic derivatives. Later, peptidomimetics and de novo designed compounds, that include up to seven chiral centres and macrocyclic rings became dominant. These drugs are prepared by total synthesis, sometimes by routes of more than 25 steps with stereocentres originating from the chiral pool, or being installed by chiral induction or enzymatic resolution. Interestingly, ring-closing metathesis proved to be the method of choice for macrocyclisation in hepatitis C virus protease inhibitors. We conclude that structural simplification, planning of synthetic routes regarding incorporation of stereocentres and macrocyclisation, as well as incorporation of structural knowledge and consideration of chameleonic properties in design, should facilitate drug discovery in bRo5 space.


Assuntos
Descoberta de Drogas , Preparações Farmacêuticas/síntese química , Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Sítios de Ligação , Hepacivirus/enzimologia , Compostos Macrocíclicos/síntese química , Compostos Macrocíclicos/química , Compostos Macrocíclicos/metabolismo , Peptidomiméticos , Preparações Farmacêuticas/química , Preparações Farmacêuticas/metabolismo , Inibidores de Proteases/síntese química , Inibidores de Proteases/química , Inibidores de Proteases/metabolismo , Ribossomos/química , Ribossomos/metabolismo , Proteínas Virais/química , Proteínas Virais/metabolismo
5.
Chem Commun (Camb) ; 56(3): 360-363, 2020 Jan 02.
Artigo em Inglês | MEDLINE | ID: mdl-31825399

RESUMO

A crystalline biohybrid with a 4 : 1 protein : cucurbituril mass ratio is presented. This result was achieved by engineering additional cucurbit[7]uril (Q7) binding sites into a ß-propeller protein. In contrast to the parent protein, Q7-controlled assembly of the engineered variant occurred in solution, as evidenced by NMR and SAXS measurements.


Assuntos
Proteínas de Bactérias/química , Hidrocarbonetos Aromáticos com Pontes/química , Imidazóis/química , Sequência de Aminoácidos , Proteínas de Bactérias/metabolismo , Sítios de Ligação , Hidrocarbonetos Aromáticos com Pontes/metabolismo , Imidazóis/metabolismo , Lectinas/química , Lectinas/genética , Lectinas/metabolismo , Ressonância Magnética Nuclear Biomolecular , Ralstonia solanacearum/metabolismo , Espalhamento a Baixo Ângulo , Difração de Raios X
6.
J Photochem Photobiol B ; 202: 111671, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31731076

RESUMO

As a molecular chaperone, ß-casein is difficult to form amyloid fibrils under physiological conditions due to its chaperone activity. Heparan sulfate (HS) has drawn attention of technologists all over the word because of its relation to amyloid deposits in some amyloidosis diseases. For better understanding the relationship between the ß-casein and HS, the multi-spectroscopic studies were employed. The data of thioflavin T (ThT) binding assay, transmission electron microscopy (TEM) and circular dichroism (CD) demonstrated that HS promoted fibril formation by ß-casein in the amount and the growth speed. The results of steady-state UV-vis absorption spectra, fluorescence spectroscopy and fluorescence lifetime revealed that the ß-casein-HS complexes were formed and HS quenched the fluorescence of ß-casein by a static quenching mechanism. On the basis of fluorescence analysis, the value of binding constant was equal to 1.17 × 107 L mol-1 at 338.15 K and there was about one binding site between them. According to thermodynamic parameters obtained, it was deduced that a spontaneous reaction happened, and protein-ligand complex was stabilized by hydrogen bonds and hydrophobic interaction. Furthermore, using fluorescence resonance energy transfer (FRET) assay, the value of binding distance between HS and Trp143 of ß-casein was calculated to be 0.93 nm. Finally, on the basis of synchronous fluorescence experiment, the polarity increasing and hydrophobicity decreasing around Trp143 occurred during the period of fibril formation by ß-casein.


Assuntos
Amiloide/metabolismo , Caseínas/química , Heparitina Sulfato/química , Amiloide/química , Animais , Sítios de Ligação , Caseínas/metabolismo , Bovinos , Dicroísmo Circular , Transferência Ressonante de Energia de Fluorescência , Heparitina Sulfato/metabolismo , Interações Hidrofóbicas e Hidrofílicas , Microscopia Eletrônica de Transmissão , Ligação Proteica , Termodinâmica
7.
J Enzyme Inhib Med Chem ; 35(1): 139-144, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31724435

RESUMO

A series of naphthalene-chalcone derivatives (3a-3t) were prepared and evaluated as tubulin polymerisation inhibitor for the treatment of breast cancer. All compounds were evaluated for their antiproliferative activity against MCF-7 cell line. The most of compounds displayed potent antiproliferative activity. Among them, compound 3a displayed the most potent antiproliferative activity with an IC50 value of 1.42 ± 0.15 µM, as compared to cisplatin (IC50 = 15.24 ± 1.27 µM). Additionally, the promising compound 3a demonstrated relatively lower cytotoxicity on normal cell line (HEK293) compared to tumour cell line. Furthermore, compound 3a was found to induce significant cell cycle arrest at the G2/M phase and cell apoptosis. Compound 3a displayed potent tubulin polymerisation inhibitory activity with an IC50 value of 8.4 µM, which was slightly more active than the reference compound colchicine (IC50 = 10.6 µM). Molecular docking analysis suggested that 3a interact and bind at the colchicine binding site of the tubulin.


Assuntos
Antineoplásicos/farmacologia , Neoplasias da Mama/tratamento farmacológico , Chalconas/farmacologia , Naftalenos/farmacologia , Moduladores de Tubulina/farmacologia , Tubulina (Proteína)/metabolismo , Antineoplásicos/síntese química , Antineoplásicos/química , Apoptose/efeitos dos fármacos , Sítios de Ligação/efeitos dos fármacos , Neoplasias da Mama/metabolismo , Neoplasias da Mama/patologia , Pontos de Checagem do Ciclo Celular/efeitos dos fármacos , Proliferação de Células/efeitos dos fármacos , Chalconas/química , Colchicina/antagonistas & inibidores , Colchicina/metabolismo , Relação Dose-Resposta a Droga , Ensaios de Seleção de Medicamentos Antitumorais , Feminino , Humanos , Células MCF-7 , Modelos Moleculares , Estrutura Molecular , Naftalenos/química , Relação Estrutura-Atividade , Moduladores de Tubulina/síntese química , Moduladores de Tubulina/química
8.
Biophys Chem ; 256: 106270, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31706136

RESUMO

DNA strands can be designed to assemble into stable three-dimensional structures, based on Watson-Crick base pairing rules. The simplest of these is the DNA tetrahedron that is composed of four oligonucleotides. We have re-designed the sequence of a DNA tetrahedron so that it contains a single (AATT) binding site for the minor groove binding ligand Hoechst 33258. We examined the stability of this structure by placing fluorescent groups within each of its edges and have shown that all the edges melt at the same temperature in the absence of the ligand. The minor groove ligand still binds to its recognition sequence within the tetrahedron and increases the melting temperature of the folded complex. This ligand-induced stabilisation is propagated into the adjacent helical arms and the tetrahedron melts as a single entity in a cooperative fashion.


Assuntos
DNA/química , Ligantes , Sequência de Bases , Sítios de Ligação , Bisbenzimidazol/química , Bisbenzimidazol/metabolismo , Conformação de Ácido Nucleico , Transição de Fase/efeitos da radiação , Espectrometria de Fluorescência , Temperatura de Transição , Raios Ultravioleta
9.
Biophys Chem ; 256: 106268, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31707064

RESUMO

Carbon nanotubes (CNTs) are extensively used in the area of biotechnology and biomedicine, and the binding of proteins to CNTs plays an important role in the potential toxicity of nanomaterials. Rutin is a glycoside of the bioactive quercetin with various health-improving effects due to its antioxidant ability. Demonstration of the interaction between serum albumin and bioactive components is important to design effective carriers for the suppression of CNTs' toxicity. In this study, bindings of bovine serum albumin (BSA) to single-walled CNTs and/or rutin were investigated by fluorescence and molecular docking techniques. The fluorescence of BSA was significantly quenched by both CNTs and rutin in static mode, which was confirmed by the Stern-Volmer calculations. Although rutin showed higher affinity to protein than CNTs, the interactions of both components with BSA did mainly locate within subdomain IIA (site I). BSA-diligand complexes were successfully formed after the simultaneous addition of CNTs and rutin. Bioactive rutin in the BSA-diligand complex still kept strong free radical scavenging activity compared to free rutin or BSA-monoligand complex. Consistently, the cytotoxicity of CNTs and reactive oxygen species formation in endothelial cells was reduced in the BSA-diligand complexes relative to those of BSA-CNTs corona or CNTs alone, where the co-presence of rutin played an important role. These findings suggest the possibility and advantage of designing BSA-based carriers for the suppression of CNTs' toxicity in their biomedical applications.


Assuntos
Nanotubos de Carbono/química , Rutina/química , Soroalbumina Bovina/química , Animais , Antioxidantes/química , Sítios de Ligação , Bovinos , Sobrevivência Celular/efeitos dos fármacos , Células Endoteliais da Veia Umbilical Humana , Humanos , Simulação de Acoplamento Molecular , Nanotubos de Carbono/toxicidade , Estrutura Terciária de Proteína , Rutina/metabolismo , Soroalbumina Bovina/metabolismo
10.
Biophys Chem ; 256: 106281, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31756663

RESUMO

Timely and accurate diagnosis of Alzheimer's disease (AD) remains a major challenge in the medical arena. ß-amyloid (Aß) imaging techniques such as positron emission tomography and single photon emission computed tomography require the use of an imaging probe. To date, only flutemetamol, florbetaben and florbetapir have been approved for clinical use as imaging probes. Design of imaging probes requires a detailed understanding of disease mechanism(s) and receptor-ligand interaction. In this study, molecular docking, molecular dynamics and binding free energies were used to investigate the multiple binding sites exhibited by ß-amyloid fibrils. Protein atomic models 2BEG, 5KK3, 2M4J, 2LMN, 5OQV, 2NAO, 2MVX and 2MXU (protein databank codes) were used to investigate the nature and location of binding sites and binding profiles of selected molecules with known affinities. Although amyloid fibrils are known to have multiple binding sites, we demonstrated that model 2MXU possesses one site which is druggable and can bind with common scaffolds currently being used in the imaging of amyloid fibrils. Models 2NAO, 5KK3 and 2M4J revealed that even though multiple sites may be available in some fibrils, the entire protein may not have a druggable site. Molecular dynamics revealed atomic models 2MXU and 2MVX to be the least flexible among the list. The outcomes of this investigation can be translated to assist in designing novel molecules that can be used for brain imaging in Alzheimer's disease.


Assuntos
Amiloide/química , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Doença de Alzheimer/metabolismo , Doença de Alzheimer/patologia , Amiloide/metabolismo , Sítios de Ligação , Bases de Dados de Proteínas , Humanos , Ligantes , Ligação Proteica , Estrutura Terciária de Proteína
11.
Biophys Chem ; 257: 106315, 2020 02.
Artigo em Inglês | MEDLINE | ID: mdl-31841862

RESUMO

Lipocalins are a widely distributed family of extracellular proteins typically involved in the transport of small hydrophobic molecules. To gain new insights into the molecular basis that governs ligand recognition by this ancient protein family, the binding properties of the domain-swapped dimer bovine odorant binding protein (bOBP) and its monomeric mutant bOBP121G+ were characterized using calorimetric techniques and molecular dynamics simulations. Thermal unfolding profiles revealed that the isolated bOBP subunits behave as a cooperative folding unit. In addition, bOBP and bOBP121G+ exhibited similar ligand binding properties, characterized by a non-classical hydrophobic effect signature. The energetic differences in the binding of bOBP to 1-hexen-3-ol and the physiological ligand 1-octen-3-ol were strikingly larger than those observed for the interaction of other lipocalins with congeneric ligands. MD simulations revealed that the recurrent opening of transient pores in the submicrosecond timescale allows a profuse exchange of water molecules between the protein interior and the surrounding solvent. This picture contrasts with other lipocalins whose ligand-free binding cavities are devoid of solvent molecules. Furthermore, the simulations indicated that internal water molecules solvate the protein cavity suboptimally, forming fewer hydrogen bonds and having lower density and higher potential energy than bulk water molecules. Upon ligand occupation, water molecules were displaced from the binding cavity in an amount that depended on the ligand size. Taken together, calorimetric and MD-simulation results are consistent with a significant contribution of cavity desolvation to the enthalpically-driven interaction of bOBP with its hydrophobic ligands.


Assuntos
Ligantes , Receptores Odorantes/química , Solventes/química , Animais , Sítios de Ligação , Bovinos , Interações Hidrofóbicas e Hidrofílicas , Simulação de Dinâmica Molecular , Mutagênese Sítio-Dirigida , Estabilidade Proteica , Receptores Odorantes/genética , Receptores Odorantes/metabolismo , Proteínas Recombinantes/biossíntese , Proteínas Recombinantes/química , Proteínas Recombinantes/isolamento & purificação , Termodinâmica , Água/química
12.
Food Chem ; 307: 125523, 2020 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-31639572

RESUMO

Lutein is a bioactive found in dark leafy vegetables that may be used as a nutraceutical agent in foodstuff and an inhibitor of key enzymes of the human body such as those involved in the cholinergic system. However, its high hydrophobicity leads to low bioavailability and must be overcome if lutein is to be added in foods. The objective of this study was to evaluate the influence of nanoencapsulated lutein in the activity of the acetylcholinesterase enzyme. The in vitro study was carried out using water in order to evaluate the impact of encapsulation on the hydrophilicity of lutein. In vitro assays showed that lutein, both free and nanoencapsulated, presented a mixed-type inhibition behavior, and encapsulated lutein was able to inhibit acetylcholinesterase activity even in an aqueous medium. Inhibition was also showed by the in silico docking results which show that lutein interacted with the pocket region of the enzyme.


Assuntos
Acetilcolinesterase/metabolismo , Cápsulas/química , Luteína/química , Simulação de Acoplamento Molecular , Nanopartículas/química , Acetilcolinesterase/química , Sítios de Ligação , Suplementos Nutricionais/análise , Humanos , Interações Hidrofóbicas e Hidrofílicas , Cinética , Luteína/metabolismo , Estrutura Terciária de Proteína
13.
Food Chem ; 305: 125463, 2020 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-31520921

RESUMO

Protein conformation and the 3D water structure play important roles in the ability of bovine serum albumin (BSA) to form stable nanostructures with bioactive molecules. We studied the influence of BSA unfolding and those of two Hofmeister salts, sodium chloride (NaCl) as kosmotrope and sodium thiocyanate (NaSCN) as chaotrope, on BSA/lutein binding at pH 7.4 using fluorescence spectroscopy. The BSA/lutein complex formation was entropically driven and lutein was preferentially bound to site III of BSA. The binding constant (104 L mol-1), complex stoichiometry (1:1), and thermodynamic potential for BSA/lutein binding were independent of protein conformation and Hofmeister salts. However, the enthalpic and entropic components of BSA/lutein binding in the presence of NaSCN decreased as the temperature increased. The opposite was observed for BSA/lutein binding in the presence of NaCl and for denatured BSA/lutein binding. Therefore, the BSA conformation and 3D water structure directly affected the BSA/lutein binding thermodynamics.


Assuntos
Luteína/metabolismo , Sais/química , Soroalbumina Bovina/metabolismo , Animais , Sítios de Ligação , Bovinos , Luteína/química , Ligação Proteica , Conformação Proteica , Soroalbumina Bovina/química , Cloreto de Sódio/química , Espectrometria de Fluorescência , Temperatura Ambiente , Termodinâmica , Tiocianatos/química
14.
Phys Chem Chem Phys ; 22(1): 203-211, 2019 Dec 18.
Artigo em Inglês | MEDLINE | ID: mdl-31799519

RESUMO

The formation of amyloid fibrils by α-synuclein (αS) protein inside the Lewy bodies and Lewy neurites is the prominent pathological hallmark of Parkinson's disease (PD). The fibrillation of αS in vitro is described by a nucleation-elongation process involving the formation of a critical nucleus. Finding the critical/smallest nuclei and effective inhibitors of αS aggregation is a crucial step for the development of drugs against PD. Recent experiments reported that dopamine (DA) and norepinephrine (NE), two prominent naturally occurring neurotransmitters, can effectively disrupt the preformed αS fibrils. The level of DA/NE in blood can be markedly increased by exercise. However, the size and structure of the critical nucleus and the disruptive mechanism by DA/NE are largely unknown. In this work, we performed multiple molecular dynamics (MD) simulations to find the critical nucleus size and examine the influences of DA/NE molecules on preformed αS44-96 (Greek-key-like core of full length αS) protofibrils. Our results show that the trimer is the critical nucleus for the αS44-96 fibril formation, and the tetramer is the minimal stable nucleus. When DA/NE molecules bind to the fibril-like trimer and tetramer, they strongly destabilize the αS protofibrils by disrupting the ß-sheet structure and inter-chain E46-K80 salt bridges. Two common binding sites are identified for both DA and NE molecules on αS oligomers: residues 57-70 and 81-83. A different binding site is also observed, which is located at the N-terminal region (residues 45-52). The binding of DA/NE molecules to αS oligomers is mostly driven by hydrophobic and electrostatic interactions. We found two disruptive modes, and binding to the turn region of αS oligomers but disrupting the adjacent ß-sheet structure is the dominant one. Our work identified the critical nucleus of Greek-key-like core of αS protofibrils and revealed the disruptive mechanism of αS protofibrils by DA/NE molecules, which may be helpful to the design of effective drugs against αS aggregation.


Assuntos
Dopamina/química , Norepinefrina/química , alfa-Sinucleína/química , Amiloide/metabolismo , Sítios de Ligação , Humanos , Simulação de Dinâmica Molecular , Norepinefrina/metabolismo , Ligação Proteica , Conformação Proteica , Eletricidade Estática
15.
Curr Top Med Chem ; 19(26): 2378-2392, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31833462

RESUMO

G protein-coupled receptors (GPCRs) represent the largest family of proteins targeted by drug design and discovery efforts. Of these efforts, the development of GPCR agonists is highly desirable, due to their therapeutic robust utility in treating diseases caused by deficient receptor signaling. One of the challenges in designing potent and selective GPCR agonists lies in the inability to achieve combined high binding affinity and subtype selectivity, due to the high homology between orthosteric sites among GPCR subtypes. To combat this difficulty, researchers have begun to explore the utility of targeting topographically distinct and less conserved binding sites, namely "allosteric" sites. Pursuing these sites offers the benefit of achieving high subtype selectivity, however, it also can result in a decreased binding affinity and potency as compared to orthosteric agonists. Therefore, bitopic ligands comprised of an orthosteric agonist and an allosteric modulator connected by a spacer and allowing binding with both the orthosteric and allosteric sites within one receptor, have been developed. It may combine the high subtype selectivity of an allosteric modulator with the high binding affinity of an orthosteric agonist and provides desired advantages over orthosteric agonists or allosteric modulators alone. Herein, we review the recent advances in the development of bitopic agonists/activators for various GPCR targets and their novel therapeutic potentials.


Assuntos
Desenvolvimento de Medicamentos/métodos , Receptores Acoplados a Proteínas-G/agonistas , Sítio Alostérico , Sequência de Aminoácidos , Animais , Sítios de Ligação , Humanos , Ligantes , Receptores Acoplados a Proteínas-G/química , Homologia de Sequência de Aminoácidos
17.
J Chem Phys ; 151(23): 235101, 2019 Dec 21.
Artigo em Inglês | MEDLINE | ID: mdl-31864244

RESUMO

Association of proteins and other biopolymers is a ubiquitous process in living systems. Recent single-molecule measurements probe the dynamics of association in unprecedented detail by measuring the properties of association transition paths, i.e., short segments of molecular trajectories between the time the proteins are close enough to interact and the formation of the final complex. Interpretation of such measurements requires adequate models for describing the dynamics of experimental observables. In an effort to develop such models, here we report a simulation study of the association dynamics of two oppositely charged, disordered polymers. We mimic experimental measurements by monitoring intermonomer distances, which we treat as "experimental reaction coordinates." While the dynamics of the distance between the centers of mass of the molecules is found to be memoryless and diffusive, the dynamics of the experimental reaction coordinates displays significant memory and can be described by a generalized Langevin equation with a memory kernel. We compute the most commonly measured property of transition paths, the distribution of the transition path time, and show that, despite the non-Markovianity of the underlying dynamics, it is well approximated as one-dimensional diffusion in the potential of mean force provided that an apparent value of the diffusion coefficient is used. This apparent value is intermediate between the slow (low frequency) and fast (high frequency) limits of the memory kernel. We have further studied how the mean transition path time depends on the ionic strength and found only weak dependence despite strong electrostatic attraction between the polymers.


Assuntos
Proteínas Intrinsicamente Desordenadas/química , Simulação de Dinâmica Molecular , Sítios de Ligação
18.
Biophys Chem ; 255: 106264, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-31670159

RESUMO

The molecular mechanisms regulating the complex sensory system that underlies olfaction are still not completely understood. The compounds formed from the interaction of Olfactory Receptors (ORs) with volatile molecules play a crucial role in producing the sense of olfaction. Therefore, it is necessary to investigate the binding mechanisms between these receptors and small ligands. In this work, we focus our attention on C.elegans, this is a particularly suitable model organism because it is characterized by a nervous system composed of only 302 neurons. To study olfaction in C.elegans, we select 21 ORs from its olfactory neurons, and present a pipeline, consisting of several computational methods, with the aim of proposing a set of possible candidates for binding the selected C.elegans ORs. This pipeline introduces an approach based on the selection of templates, and threading, that takes advantage of the structural redundancy among membrane receptors. This procedure is widely replicable because it is based on algorithms that are publicly available and are freely hosted on institutional servers.


Assuntos
Proteínas de Caenorhabditis elegans/química , Caenorhabditis elegans/metabolismo , Odorantes/análise , Receptores Odorantes/química , Animais , Sítios de Ligação , Proteínas de Caenorhabditis elegans/metabolismo , Bases de Dados de Proteínas , Simulação de Acoplamento Molecular , Ligação Proteica , Estrutura Terciária de Proteína , Receptores Odorantes/metabolismo
19.
J Chem Theory Comput ; 15(12): 7004-7014, 2019 Dec 10.
Artigo em Inglês | MEDLINE | ID: mdl-31670957

RESUMO

N6-Methyladenosine (m6A) is the most prevalent chemical modification in human mRNAs. Its recognition by reader proteins enables many cellular functions, including splicing and translation of mRNAs. However, the binding mechanisms of m6A-containing RNAs to their readers are still elusive due to the unclear roles of m6A-flanking ribonucleotides. Here, we use a model system, YTHDC1 with its RNA motif 5'-G-2G-1(m6A)C+1U+2-3', to investigate the binding mechanisms by atomistic simulations, X-ray crystallography, and isothermal titration calorimetry. The experimental data and simulation results show that m6A is captured by an aromatic cage of YTHDC1 and the 3' terminus nucleotides are stabilized by cation-π-π interactions, while the 5' terminus remains flexible. Notably, simulations of unbound RNA motifs reveal that the methyl group of m6A and the 5' terminus shift the conformational preferences of the oligoribonucleotide to the bound-like conformation, thereby facilitating the association process. The binding mechanisms may help in the discovery of chemical probes against m6A reader proteins.


Assuntos
Proteínas do Tecido Nervoso/química , Motivos de Nucleotídeos , Fatores de Processamento de RNA/química , RNA Mensageiro/química , Sítios de Ligação , Cristalografia por Raios X , Humanos , Modelos Moleculares , Proteínas do Tecido Nervoso/isolamento & purificação , Fatores de Processamento de RNA/isolamento & purificação
20.
Biochemistry (Mosc) ; 84(10): 1177-1185, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31694513

RESUMO

It was previously shown that hemagglutinin residues Thr155, Glu158, and Ser228 are crucial for the recognition of Neu5Gc. In this study, we demonstrated that the ability to bind the Neu5Gc-terminated receptor is related to the amino acid 145: viruses of years 1972-1999 with Lys145 bind to the receptor, whereas viruses with Asn145 do not. Sporadic appearance and disappearance of the ability to bind Neu5Gc oligosaccharides and the absence of Neu5Gc in the composition of human glycoconjugates indicate the non-adaptive nature of this ability. It was previously shown that unlike H1N1 viruses, H3N2 viruses of years 1968-1989 did not distinguish between Neu5Acα2-6Galß1-4Glc (6'SL) and Neu5Acα2-6Galß1-4GlcNAc (6'SLN). H3N2 viruses isolated after 1993 have acquired the ability to distinguish between 6'SL and 6'SLN, similarly to H1N1 viruses. We found that the affinity for 6'SLN has gradually increased from 1992 to 2003. After 2003, the viruses lost the ability to bind a number of sialosides, including 6'SL, that were good receptors for earlier H3N2 viruses, and retained high affinity for 6'SLN only, which correlated with the acquisition of new glycosylation sites at positions 122, 133, and 144, as well as Glu190Asp and Gly225Asp substitutions, in hemagglutinin. These substitutions are also responsible for the receptor-binding phenotype of human H1N1 viruses. We conclude that the convergent evolution of the receptor specificity of the H1N1 and H3N2 viruses indicates that 6'SLN is the optimal natural human receptor for influenza viruses.


Assuntos
Vírus da Influenza A Subtipo H3N2/química , Receptores Virais/química , Sítios de Ligação , Humanos , Vírus da Influenza A Subtipo H3N2/genética , Vírus da Influenza A Subtipo H3N2/metabolismo , Receptores Virais/sangue
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