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1.
Int J Mol Sci ; 22(5)2021 Feb 26.
Artigo em Inglês | MEDLINE | ID: mdl-33652858

RESUMO

Alzheimer's disease (AD) is a neurodegenerative disease characterized by severe brain damage and dementia. There are currently few therapeutics to treat this disease, and they can only temporarily alleviate some of the symptoms. The pathogenesis of AD is mainly preceded by accumulation of abnormal amyloid beta (Aß) aggregates, which are toxic to neurons. Therefore, modulation of the formation of these abnormal aggregates is strongly suggested as the most effective approach to treat AD. In particular, numerous studies on natural products associated with AD, aiming to downregulate Aß peptides and suppress the formation of abnormal Aß aggregates, thus reducing neural cell death, are being conducted. Generation of Aß peptides can be prevented by targeting the secretases involved in Aß-peptide formation (secretase-dependent). Additionally, blocking the intra- and intermolecular interactions of Aß peptides can induce conformational changes in abnormal Aß aggregates, whereby the toxicity can be ameliorated (structure-dependent). In this review, AD-associated natural products which can reduce the accumulation of Aß peptides via secretase- or structure-dependent pathways, and the current clinical trial states of these products are discussed.


Assuntos
Doença de Alzheimer/tratamento farmacológico , Peptídeos beta-Amiloides/metabolismo , Produtos Biológicos/farmacologia , Doença de Alzheimer/metabolismo , Secretases da Proteína Precursora do Amiloide/metabolismo , Animais , Produtos Biológicos/química , Descoberta de Drogas , Humanos , Terapia de Alvo Molecular , Agregados Proteicos/efeitos dos fármacos , Conformação Proteica/efeitos dos fármacos , Transdução de Sinais/efeitos dos fármacos
2.
Elife ; 102021 02 11.
Artigo em Inglês | MEDLINE | ID: mdl-33570492

RESUMO

Bovines have evolved a subset of antibodies with ultra-long heavy chain complementarity determining regions that harbour cysteine-rich knob domains. To produce high-affinity peptides, we previously isolated autonomous 3-6 kDa knob domains from bovine antibodies. Here, we show that binding of four knob domain peptides elicits a range of effects on the clinically validated drug target complement C5. Allosteric mechanisms predominated, with one peptide selectively inhibiting C5 cleavage by the alternative pathway C5 convertase, revealing a targetable mechanistic difference between the classical and alternative pathway C5 convertases. Taking a hybrid biophysical approach, we present C5-knob domain co-crystal structures and, by solution methods, observed allosteric effects propagating >50 Å from the binding sites. This study expands the therapeutic scope of C5, presents new inhibitors, and introduces knob domains as new, low molecular weight antibody fragments, with therapeutic potential.


Assuntos
Regulação Alostérica/efeitos dos fármacos , Complemento C5/antagonistas & inibidores , Descoberta de Drogas , Peptídeos/química , Peptídeos/farmacologia , Animais , Bovinos , Complemento C5/química , Complemento C5/metabolismo , Simulação de Acoplamento Molecular , Conformação Proteica/efeitos dos fármacos
3.
Nature ; 590(7846): 509-514, 2021 02.
Artigo em Inglês | MEDLINE | ID: mdl-33568813

RESUMO

Mechanosensitive channels sense mechanical forces in cell membranes and underlie many biological sensing processes1-3. However, how exactly they sense mechanical force remains under investigation4. The bacterial mechanosensitive channel of small conductance, MscS, is one of the most extensively studied mechanosensitive channels4-8, but how it is regulated by membrane tension remains unclear, even though the structures are known for its open and closed states9-11. Here we used cryo-electron microscopy to determine the structure of MscS in different membrane environments, including one that mimics a membrane under tension. We present the structures of MscS in the subconducting and desensitized states, and demonstrate that the conformation of MscS in a lipid bilayer in the open state is dynamic. Several associated lipids have distinct roles in MscS mechanosensation. Pore lipids are necessary to prevent ion conduction in the closed state. Gatekeeper lipids stabilize the closed conformation and dissociate with membrane tension, allowing the channel to open. Pocket lipids in a solvent-exposed pocket between subunits are pulled out under sustained tension, allowing the channel to transition to the subconducting state and then to the desensitized state. Our results provide a mechanistic underpinning and expand on the 'force-from-lipids' model for MscS mechanosensation4,11.


Assuntos
Microscopia Crioeletrônica , Proteínas de Escherichia coli/metabolismo , Proteínas de Escherichia coli/ultraestrutura , Escherichia coli/química , Canais Iônicos/metabolismo , Canais Iônicos/ultraestrutura , Membranas Artificiais , Fosfatidilcolinas/metabolismo , Detergentes/farmacologia , Escherichia coli/ultraestrutura , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/genética , Interações Hidrofóbicas e Hidrofílicas , Canais Iônicos/química , Canais Iônicos/genética , Bicamadas Lipídicas/química , Bicamadas Lipídicas/metabolismo , Mecanotransdução Celular/efeitos dos fármacos , Modelos Moleculares , Mutação , Nanoestruturas/química , Nanoestruturas/ultraestrutura , Fosfatidilcolinas/química , Fosfatidilcolinas/farmacologia , Conformação Proteica/efeitos dos fármacos , beta-Ciclodextrinas/farmacologia
4.
Nat Commun ; 12(1): 582, 2021 01 25.
Artigo em Inglês | MEDLINE | ID: mdl-33495441

RESUMO

Tumour necrosis factor (TNF) is a trimeric protein which signals through two membrane receptors, TNFR1 and TNFR2. Previously, we identified small molecules that inhibit human TNF by stabilising a distorted trimer and reduce the number of receptors bound to TNF from three to two. Here we present a biochemical and structural characterisation of the small molecule-stabilised TNF-TNFR1 complex, providing insights into how a distorted TNF trimer can alter signalling function. We demonstrate that the inhibitors reduce the binding affinity of TNF to the third TNFR1 molecule. In support of this, we show by X-ray crystallography that the inhibitor-bound, distorted, TNF trimer forms a complex with a dimer of TNFR1 molecules. This observation, along with data from a solution-based network assembly assay, leads us to suggest a model for TNF signalling based on TNF-TNFR1 clusters, which are disrupted by small molecule inhibitors.


Assuntos
Multimerização Proteica/efeitos dos fármacos , Receptores Tipo I de Fatores de Necrose Tumoral/química , Transdução de Sinais/efeitos dos fármacos , Bibliotecas de Moléculas Pequenas/farmacologia , Fator de Necrose Tumoral alfa/química , Algoritmos , Animais , Ligação Competitiva/efeitos dos fármacos , Humanos , Modelos Moleculares , Ligação Proteica/efeitos dos fármacos , Conformação Proteica/efeitos dos fármacos , Receptores Tipo I de Fatores de Necrose Tumoral/metabolismo , Bibliotecas de Moléculas Pequenas/química , Fator de Necrose Tumoral alfa/metabolismo
5.
Nat Commun ; 12(1): 583, 2021 01 25.
Artigo em Inglês | MEDLINE | ID: mdl-33495445

RESUMO

We have recently described the development of a series of small-molecule inhibitors of human tumour necrosis factor (TNF) that stabilise an open, asymmetric, signalling-deficient form of the soluble TNF trimer. Here, we describe the generation, characterisation, and utility of a monoclonal antibody that selectively binds with high affinity to the asymmetric TNF trimer-small molecule complex. The antibody helps to define the molecular dynamics of the apo TNF trimer, reveals the mode of action and specificity of the small molecule inhibitors, acts as a chaperone in solving the human TNF-TNFR1 complex crystal structure, and facilitates the measurement of small molecule target occupancy in complex biological samples. We believe this work defines a role for monoclonal antibodies as tools to facilitate the discovery and development of small-molecule inhibitors of protein-protein interactions.


Assuntos
Anticorpos Monoclonais/metabolismo , Complexos Multiproteicos/metabolismo , Receptores Tipo I de Fatores de Necrose Tumoral/metabolismo , Bibliotecas de Moléculas Pequenas/metabolismo , Fator de Necrose Tumoral alfa/metabolismo , Anticorpos Monoclonais/farmacologia , Células Cultivadas , Cristalografia por Raios X , Epitopos/química , Epitopos/metabolismo , Células HEK293 , Humanos , Modelos Moleculares , Complexos Multiproteicos/química , Ligação Proteica/efeitos dos fármacos , Conformação Proteica/efeitos dos fármacos , Receptores Tipo I de Fatores de Necrose Tumoral/química , Transdução de Sinais/efeitos dos fármacos , Bibliotecas de Moléculas Pequenas/química , Bibliotecas de Moléculas Pequenas/farmacologia , Fator de Necrose Tumoral alfa/química
6.
Arch Biochem Biophys ; 699: 108733, 2021 03 15.
Artigo em Inglês | MEDLINE | ID: mdl-33388313

RESUMO

Muscle myosins are molecular motors that hydrolyze ATP and generate force through coordinated interactions with actin filaments, known as cross-bridge cycling. During the cross-bridge cycle, functional sites in myosin 'sense' changes in interactions with actin filaments and the nucleotide binding region, resulting in allosteric transmission of information throughout the structure. We investigated whether the dynamics of the post-powerstroke state of the cross-bridge cycle are modulated in a nucleotide-dependent fashion. We compared molecular dynamics simulations of the myosin II motor domain (M) from Dictyostelium discoideum in the presence of ADP (M.ADP) versus 2'-deoxy-ADP bound myosin (M.dADP). We found that dADP was more flexible than ADP and the two nucleotides interacted with myosin in different ways. Replacement of ADP with dADP in the post-powerstroke state also altered the conformation of the actin binding region in myosin heads. Our results provide atomic level insights into allosteric communication networks in myosin that provide insight into the nucleotide-dependent dynamics of the cross-bridge cycle.


Assuntos
Nucleotídeos de Desoxiadenina/metabolismo , Miosina Tipo II/metabolismo , Difosfato de Adenosina/química , Difosfato de Adenosina/metabolismo , Sítios de Ligação , Nucleotídeos de Desoxiadenina/química , Dictyostelium/enzimologia , Simulação de Dinâmica Molecular , Miosina Tipo II/química , Maleabilidade , Ligação Proteica , Conformação Proteica/efeitos dos fármacos , Domínios Proteicos
7.
Int J Biol Macromol ; 169: 251-263, 2021 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-33345970

RESUMO

α-Synuclein is an intrinsically disordered protein whose aggregation is related to Parkinson's disease and other neurodegenerative disorders. Metal cations are one of the main factors affecting the propensity of α-synuclein to aggregate, either by directly binding to it or by catalyzing the production of reactive oxygen species that oxidize it. His50, Asp121 and several additional C-terminal α-synuclein residues are binding sites for numerous metal cations, while methionine sulfoxidation occurs readily on this protein under oxidative stress conditions. Molecular dynamics simulations are an excellent tool to obtain a microscopic picture of how metal binding or methionine sulfoxidation alter the conformational preferences of α-synuclein and, hence, its aggregation propensity. In this work, we report the first coarse-grained molecular dynamics study comparing the conformational ensembles of the native protein, the protein bound to either Cu2+ or Ca2+ at its main binding sites, and the methionine-sulfoxidized protein. Our results suggest that these events alter the transient α-synuclein intramolecular contacts, inducing a greater solvent exposure of its hydrophobic, aggregation-prone NAC domain, in full agreement with a recent experimental study on Ca2+ binding. Moreover, metal-binding residues directly participate in the long-range contacts that shield this domain and regulate α-synuclein aggregation. These results provide a molecular-level rationalization of the enhanced fibrillation experimentally observed in the presence of Cu2+ or Ca2+ and the oligomerization induced by methionine sulfoxidation.


Assuntos
Cálcio/química , Cobre/química , alfa-Sinucleína/química , Sítios de Ligação , Cálcio/metabolismo , Catálise , Cobre/metabolismo , Humanos , Proteínas Intrinsicamente Desordenadas , Metionina/química , Metionina/metabolismo , Simulação de Dinâmica Molecular , Oxirredução , Estresse Oxidativo , Doença de Parkinson/metabolismo , Conformação Proteica/efeitos dos fármacos , alfa-Sinucleína/metabolismo
8.
Methods Mol Biol ; 2253: 245-254, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33315227

RESUMO

Allosteric drugs are ligands that when bound to an allosteric site modify the conformational state of the pharmacological target, leading then to a modification of functional response upon binding of the endogenous ligand. Pharmacological targets are defined as biological entities, to which a ligand/drug binds and leads to a functional effect. Pharmacological targets can be proteins or nucleic acids. Computational approaches such as molecular dynamics (MD) sped up discovery and identification of allosteric binding sites and allosteric ligands. Classical all-atom and hybrid classical/quantum MD simulations can be generalized as simulation techniques aimed at analysis of atoms and molecular motion. Main limitations of MD simulations are related to high computational costs, that in turn limit the conformational sampling of biological systems. Indeed, other techniques have been developed to overcome limitations of MD, such as enhanced sampling MD simulations. In this chapter, classical MD and enhanced sampling MD simulations will be described, along with their application to drug discovery, with a focus on allosteric drugs.


Assuntos
Proteínas/química , Proteínas/metabolismo , Regulação Alostérica , Sítio Alostérico , Descoberta de Drogas , Ligantes , Modelos Moleculares , Simulação de Dinâmica Molecular , Conformação Proteica/efeitos dos fármacos , Proteínas/efeitos dos fármacos , Relação Estrutura-Atividade
9.
Chem Biol Interact ; 335: 109364, 2021 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-33359597

RESUMO

Metallic nanoparticles are an important and widely used materials in development of nano-enabled medicine. For that reason, their interaction with biological molecules has to be systematically examined, as use of nanoparticles can lead to altered biological functions. In this study, we evaluated the interaction between silver nanoparticles (AgNPs) and two important plasma transport proteins - albumin and α-1-acid glycoprotein. To investigate comprehensively how different physico-chemical properties impact interaction of proteins with nanosurface, AgNPs of different size, shape and surface coating was prepared. The study was conducted using UV-Vis absorption, fluorescence, inductively coupled plasma mass spectrometry, circular dichroism spectroscopy, transmission electron microscopy, dynamic and electrophoretic light scattering techniques. The results showed significant complexities of the nano-bio interface and binding affinities of proteins onto surface of different AgNPs, which were affected by both AgNPs and protein properties. The most significant role on AgNPs-protein interaction had the coating agents used for AgNPs surface stabilization. Our findings should improve safe-by-design approach to development of the metallic nanomaterials for medical use.


Assuntos
Nanopartículas Metálicas/química , Orosomucoide/metabolismo , Soroalbumina Bovina/metabolismo , Animais , Bovinos , Orosomucoide/química , Tamanho da Partícula , Polímeros/química , Ligação Proteica , Conformação Proteica/efeitos dos fármacos , Soroalbumina Bovina/química , Prata/química , Tensoativos/química
10.
Int J Mol Sci ; 21(24)2020 Dec 13.
Artigo em Inglês | MEDLINE | ID: mdl-33322098

RESUMO

Interferon-ß (IFN-ß) is a pleiotropic cytokine used for therapy of multiple sclerosis, which is also effective in suppression of viral and bacterial infections and cancer. Recently, we reported a highly specific interaction between IFN-ß and S100P lowering IFN-ß cytotoxicity to cancer cells (Int J Biol Macromol. 2020; 143: 633-639). S100P is a member of large family of multifunctional Ca2+-binding proteins with cytokine-like activities. To probe selectivity of IFN-ß-S100 interaction with respect to S100 proteins, we used surface plasmon resonance spectroscopy, chemical crosslinking, and crystal violet assay. Among the thirteen S100 proteins studied S100A1, S100A4, and S100A6 proteins exhibit strictly Ca2+-dependent binding to IFN-ß with equilibrium dissociation constants, Kd, of 0.04-1.5 µM for their Ca2+-bound homodimeric forms. Calcium depletion abolishes the S100-IFN-ß interactions. Monomerization of S100A1/A4/A6 decreases Kd values down to 0.11-1.0 nM. Interferon-α is unable of binding to the S100 proteins studied. S100A1/A4 proteins inhibit IFN-ß-induced suppression of MCF-7 cells viability. The revealed direct influence of specific S100 proteins on IFN-ß activity uncovers a novel regulatory role of particular S100 proteins, and opens up novel approaches to enhancement of therapeutic efficacy of IFN-ß.


Assuntos
Cálcio/metabolismo , Interferon beta/metabolismo , Proteínas S100/metabolismo , Sequência de Aminoácidos , Cálcio/química , Proteínas de Ligação ao Cálcio/química , Proteínas de Ligação ao Cálcio/metabolismo , Doenças Cardiovasculares/metabolismo , Proteínas de Ciclo Celular/química , Proteínas de Ciclo Celular/metabolismo , Sobrevivência Celular/efeitos dos fármacos , Dimerização , Humanos , Cinética , Células MCF-7 , Modelos Químicos , Simulação de Acoplamento Molecular , Proteínas de Neoplasias/química , Proteínas de Neoplasias/metabolismo , Neoplasias/metabolismo , Doenças do Sistema Nervoso/metabolismo , Ligação Proteica , Conformação Proteica/efeitos dos fármacos , Proteína A6 Ligante de Cálcio S100/química , Proteína A6 Ligante de Cálcio S100/metabolismo , Proteína A4 de Ligação a Cálcio da Família S100/química , Proteína A4 de Ligação a Cálcio da Família S100/metabolismo , Proteínas S100/química , Alinhamento de Sequência , Ressonância de Plasmônio de Superfície
11.
Sci Adv ; 6(37)2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32917717

RESUMO

There is an urgent need to repurpose drugs against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Recent computational-experimental screenings have identified several existing drugs that could serve as effective inhibitors of the virus' main protease, Mpro, which is involved in gene expression and replication. Among these, ebselen (2-phenyl-1,2-benzoselenazol-3-one) appears to be particularly promising. Here, we examine, at a molecular level, the potential of ebselen to decrease Mpro activity. We find that it exhibits a distinct affinity for the catalytic region. Our results reveal a higher-affinity, previously unknown binding site localized between the II and III domains of the protein. A detailed strain analysis indicates that, on such a site, ebselen exerts a pronounced allosteric effect that regulates catalytic site access through surface-loop interactions, thereby inducing a reconfiguration of water hotspots. Together, these findings highlight the promise of ebselen as a repurposed drug against SARS-CoV-2.


Assuntos
Antivirais/farmacologia , Azóis/metabolismo , Azóis/farmacologia , Betacoronavirus/efeitos dos fármacos , Infecções por Coronavirus/tratamento farmacológico , Cisteína Endopeptidases/metabolismo , Compostos Organosselênicos/metabolismo , Compostos Organosselênicos/farmacologia , Pneumonia Viral/tratamento farmacológico , Proteínas não Estruturais Virais/metabolismo , Antivirais/metabolismo , Betacoronavirus/metabolismo , Sítios de Ligação , Domínio Catalítico/efeitos dos fármacos , Reposicionamento de Medicamentos , Humanos , Modelos Moleculares , Simulação de Dinâmica Molecular , Pandemias , Conformação Proteica/efeitos dos fármacos
12.
Int J Biol Macromol ; 164: 1693-1703, 2020 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-32745548

RESUMO

The global health emergency generated by coronavirus disease 2019 (COVID-19) has prompted the search for preventive and therapeutic treatments for its pathogen, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). There are many potential targets for drug discovery and development to tackle this disease. One of these targets is the main protease, Mpro or 3CLpro, which is highly conserved among coronaviruses. 3CLpro is an essential player in the viral replication cycle, processing the large viral polyproteins and rendering the individual proteins functional. We report a biophysical characterization of the structural stability and the catalytic activity of 3CLpro from SARS-CoV-2, from which a suitable experimental in vitro molecular screening procedure has been designed. By screening of a small chemical library consisting of about 150 compounds, the natural product quercetin was identified as reasonably potent inhibitor of SARS-CoV-2 3CLpro (Ki ~ 7 µM). Quercetin could be shown to interact with 3CLpro using biophysical techniques and bind to the active site in molecular simulations. Quercetin, with well-known pharmacokinetic and ADMET properties, can be considered as a good candidate for further optimization and development, or repositioned for COVID-19 therapeutic treatment.


Assuntos
Antivirais/farmacologia , Betacoronavirus/enzimologia , Cisteína Endopeptidases/química , Inibidores de Proteases/farmacologia , Quercetina/farmacologia , Proteínas não Estruturais Virais/antagonistas & inibidores , Proteínas não Estruturais Virais/química , Antivirais/química , Betacoronavirus/química , Betacoronavirus/efeitos dos fármacos , Domínio Catalítico/efeitos dos fármacos , Infecções por Coronavirus/tratamento farmacológico , Infecções por Coronavirus/virologia , Cisteína Endopeptidases/metabolismo , Descoberta de Drogas , Humanos , Simulação de Acoplamento Molecular , Pandemias , Pneumonia Viral/tratamento farmacológico , Pneumonia Viral/virologia , Inibidores de Proteases/química , Conformação Proteica/efeitos dos fármacos , Desdobramento de Proteína , Quercetina/química , Proteínas não Estruturais Virais/metabolismo
13.
Science ; 369(6506): 993-999, 2020 Aug 21.
Artigo em Inglês | MEDLINE | ID: mdl-32820126

RESUMO

Stimulator of interferon genes (STING) links innate immunity to biological processes ranging from antitumor immunity to microbiome homeostasis. Mechanistic understanding of the anticancer potential for STING receptor activation is currently limited by metabolic instability of the natural cyclic dinucleotide (CDN) ligands. From a pathway-targeted cell-based screen, we identified a non-nucleotide, small-molecule STING agonist, termed SR-717, that demonstrates broad interspecies and interallelic specificity. A 1.8-angstrom cocrystal structure revealed that SR-717 functions as a direct cyclic guanosine monophosphate-adenosine monophosphate (cGAMP) mimetic that induces the same "closed" conformation of STING. SR-717 displayed antitumor activity; promoted the activation of CD8+ T, natural killer, and dendritic cells in relevant tissues; and facilitated antigen cross-priming. SR-717 also induced the expression of clinically relevant targets, including programmed cell death 1 ligand 1 (PD-L1), in a STING-dependent manner.


Assuntos
Antineoplásicos/farmacologia , Materiais Biomiméticos/farmacologia , Proteínas de Membrana/metabolismo , Nucleotídeos Cíclicos/farmacologia , Animais , Antígeno B7-H1/metabolismo , Materiais Biomiméticos/química , Linfócitos T CD8-Positivos/efeitos dos fármacos , Linfócitos T CD8-Positivos/imunologia , Cristalografia por Raios X , Células Dendríticas/efeitos dos fármacos , Células Dendríticas/imunologia , Humanos , Células Matadoras Naturais/efeitos dos fármacos , Células Matadoras Naturais/imunologia , Camundongos , Nucleotídeos Cíclicos/química , Conformação Proteica/efeitos dos fármacos
15.
Nat Struct Mol Biol ; 27(8): 726-734, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32601441

RESUMO

The HIV-1 envelope glycoprotein (Env) trimer, composed of gp120 and gp41 subunits, mediates viral entry into cells. Recombinant Env trimers have been studied structurally, but characterization of Env embedded in intact virus membranes has been limited to low resolution. Here, we deploy cryo-electron tomography and subtomogram averaging to determine the structures of Env trimers on aldrithiol-2 (AT-2)-inactivated virions in ligand-free, antibody-bound and CD4-bound forms at subnanometer resolution. Tomographic reconstructions document molecular features consistent with high-resolution structures of engineered soluble and detergent-solubilized Env trimers. One of three conformational states previously predicted by smFRET was not observed by cryo-ET, potentially owing to AT-2 inactivation. We did observe Env trimers to open in situ in response to CD4 binding, with an outward movement of gp120-variable loops and an extension of a critical gp41 helix. Overall features of Env trimer embedded in AT-2-treated virions appear well-represented by current engineered trimers.


Assuntos
2,2'-Dipiridil/análogos & derivados , Dissulfetos/farmacologia , Proteína gp120 do Envelope de HIV/química , Proteína gp41 do Envelope de HIV/química , HIV-1/efeitos dos fármacos , Vírion/efeitos dos fármacos , 2,2'-Dipiridil/farmacologia , Linhagem Celular , Microscopia Crioeletrônica , Tomografia com Microscopia Eletrônica , Proteína gp120 do Envelope de HIV/ultraestrutura , Proteína gp41 do Envelope de HIV/ultraestrutura , Infecções por HIV/virologia , HIV-1/química , Humanos , Modelos Moleculares , Oxidantes/farmacologia , Conformação Proteica/efeitos dos fármacos , Multimerização Proteica/efeitos dos fármacos , Solubilidade , Vírion/química
16.
Int J Biol Macromol ; 164: 66-76, 2020 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-32693122

RESUMO

The global outbreak of COVID-19 (Coronavirus Disease 2019) caused by SARS-CoV-2 (Severe Acute Respiratory Syndrome caused by Coronavirus 2) began in December 2019. Its closest relative, SARS-CoV-1, has a slightly mutated Spike (S) protein, which interacts with ACE2 receptor in human cells to start the infection. So far, there are no vaccines or drugs to treat COVID-19. So, research groups worldwide are seeking new molecules targeting the S protein to prevent infection by SARS-CoV-2 and COVID-19 establishment. We performed molecular docking analysis of eight synthetic peptides against SARS-CoV-2 S protein. All interacted with the protein, but Mo-CBP3-PepII and PepKAA had the highest affinity with it. By binding to the S protein, both peptides led to conformational alterations in the protein, resulting in incorrect interaction with ACE2. Therefore, given the importance of the S protein-ACE2 interaction for SARS-CoV-2 infection, synthetic peptides could block SARS-CoV-2 infection. Moreover, unlike other antiviral drugs, peptides have no toxicity to human cells. Thus, these peptides are potential molecules to be tested against SARS-CoV-2 and to develop new drugs to treat COVID-19.


Assuntos
Antivirais/farmacologia , Betacoronavirus/química , Infecções por Coronavirus/tratamento farmacológico , Peptídeos/farmacologia , Peptidil Dipeptidase A/química , Pneumonia Viral/tratamento farmacológico , Glicoproteína da Espícula de Coronavírus/química , Antivirais/química , Betacoronavirus/efeitos dos fármacos , Betacoronavirus/metabolismo , Sítios de Ligação/efeitos dos fármacos , Biologia Computacional , Infecções por Coronavirus/metabolismo , Infecções por Coronavirus/virologia , Humanos , Simulação de Acoplamento Molecular , Pandemias , Peptídeos/química , Peptidil Dipeptidase A/metabolismo , Pneumonia Viral/metabolismo , Pneumonia Viral/virologia , Ligação Proteica/efeitos dos fármacos , Conformação Proteica/efeitos dos fármacos , Domínios e Motivos de Interação entre Proteínas/efeitos dos fármacos , Glicoproteína da Espícula de Coronavírus/metabolismo
17.
Mol Pharmacol ; 98(4): 475-486, 2020 10.
Artigo em Inglês | MEDLINE | ID: mdl-32680919

RESUMO

Methadone is a synthetic opioid agonist with notoriously unique properties, such as lower abuse liability and induced relief of withdrawal symptoms and drug cravings, despite acting on the same opioid receptors triggered by classic opioids-in particular the µ-opioid receptor (MOR). Its distinct pharmacologic properties, which have recently been attributed to the preferential activation of ß-arrestin over G proteins, make methadone a standard-of-care maintenance medication for opioid addiction. Although a recent biophysical study suggests that methadone stabilizes different MOR active conformations from those stabilized by classic opioid drugs or G protein-biased agonists, how this drug modulates the conformational equilibrium of MOR and what specific active conformation of the receptor it stabilizes are unknown. Here, we report the results of submillisecond adaptive sampling molecular dynamics simulations of a predicted methadone-bound MOR complex and compare them with analogous data obtained for the classic opioid morphine and the G protein-biased ligand TRV130. The model, which is supported by existing experimental data, is analyzed using Markov state models and transfer entropy analysis to provide testable hypotheses of methadone-specific conformational dynamics and activation kinetics of MOR. SIGNIFICANCE STATEMENT: Opioid addiction has reached epidemic proportions in both industrialized and developing countries. Although methadone maintenance treatment represents an effective therapeutic approach for opioid addiction, it is not as widely used as needed. In this study, we contribute an atomic-level understanding of how methadone exerts its unique function in pursuit of more accessible treatments for opioid addiction. In particular, we present details of a methadone-specific active conformation of the µ-opioid receptor that has thus far eluded experimental structural characterization.


Assuntos
Analgésicos Opioides/farmacologia , Metadona/farmacologia , Receptores Opioides mu/química , Receptores Opioides mu/metabolismo , Compostos de Espiro/farmacologia , Tiofenos/farmacologia , Analgésicos Opioides/química , Animais , Sítios de Ligação , Entropia , Humanos , Cadeias de Markov , Metadona/química , Camundongos , Modelos Moleculares , Simulação de Dinâmica Molecular , Ligação Proteica , Conformação Proteica/efeitos dos fármacos , Compostos de Espiro/química , Tiofenos/química
18.
J Recept Signal Transduct Res ; 40(6): 605-612, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-32476594

RESUMO

Recently, a pathogen has been identified as a novel coronavirus (SARS-CoV-2) and found to trigger novel pneumonia (COVID-19) in human beings and some other mammals. The uncontrolled release of cytokines is seen from the primary stages of symptoms to last acute respiratory distress syndrome (ARDS). Thus, it is necessary to find out safe and effective drugs against this deadly coronavirus as soon as possible. Here, we downloaded the three-dimensional model of NSP10/NSP16 methyltransferase (PDB-ID: 6w6l) and main protease (PDB-ID: 6lu7) of COVID-19. Using these molecular models, we performed virtual screening with our anti-viral, inti-infectious, and anti-protease compounds, which are attractive therapeutics to prevent infection of the COVID-19. We found that top screened compound binds with protein molecules with good dock score with the help of hydrophobic interactions and hydrogen bonding. We observed that protease complexed with Cyclocytidine hydrochloride (anti-viral and anti-cancer), Trifluridine (anti-viral), Adonitol, and Meropenem (anti-bacterial), and Penciclovir (anti-viral) bound with a good docking score ranging from -6.8 to -5.1 (Kcal/mol). Further, NSP10/NSP16 methyltransferase complexed with Telbivudine, Oxytetracycline dihydrate (anti-viral), Methylgallate (anti-malarial), 2-deoxyglucose and Daphnetin (anti-cancer) from the docking score of -7.0 to -5.7 (Kcal/mol). In conclusion, the selected compounds may be used as a novel therapeutic agent to combat this deadly pandemic disease, SARS-CoV-2 infection, but needs further experimental research.HighlightsNSP10/NSP16 methyltransferase and main protease complex of SARS CoV-2 bind with selected drugs.NSP10/NSP16 methyltransferase and protease interacted with drugs by hydrophobic interactions.Compounds show good DG binging free energy with protein complexes.Ligands were found to follow the Lipinski rule of five.


Assuntos
Antivirais/química , Infecções por Coronavirus/tratamento farmacológico , Pneumonia Viral/tratamento farmacológico , Proteínas não Estruturais Virais/química , Proteínas Virais Reguladoras e Acessórias/química , Aciclovir/análogos & derivados , Aciclovir/química , Aciclovir/uso terapêutico , Ancitabina/química , Ancitabina/uso terapêutico , Antivirais/uso terapêutico , Betacoronavirus/efeitos dos fármacos , Betacoronavirus/patogenicidade , Infecções por Coronavirus/virologia , Avaliação Pré-Clínica de Medicamentos , Guanina , Humanos , Meropeném/química , Meropeném/uso terapêutico , Modelos Moleculares , Simulação de Acoplamento Molecular , Pandemias , Pneumonia Viral/virologia , Conformação Proteica/efeitos dos fármacos , Ribitol/química , Ribitol/uso terapêutico , Trifluridina/química , Trifluridina/uso terapêutico , Interface Usuário-Computador , Proteínas não Estruturais Virais/antagonistas & inibidores , Proteínas não Estruturais Virais/ultraestrutura , Proteínas Virais Reguladoras e Acessórias/antagonistas & inibidores , Proteínas Virais Reguladoras e Acessórias/ultraestrutura
19.
ACS Comb Sci ; 22(6): 297-305, 2020 06 08.
Artigo em Inglês | MEDLINE | ID: mdl-32402186

RESUMO

A new coronavirus (CoV) caused a pandemic named COVID-19, which has become a global health care emergency in the present time. The virus is referred to as SARS-CoV-2 (severe acute respiratory syndrome-coronavirus-2) and has a genome similar (∼82%) to that of the previously known SARS-CoV (SARS coronavirus). An attractive therapeutic target for CoVs is the main protease (Mpro) or 3-chymotrypsin-like cysteine protease (3CLpro), as this enzyme plays a key role in polyprotein processing and is active in a dimeric form. Further, Mpro is highly conserved among various CoVs, and a mutation in Mpro is often lethal to the virus. Thus, drugs targeting the Mpro enzyme significantly reduce the risk of mutation-mediated drug resistance and display broad-spectrum antiviral activity. The combinatorial design of peptide-based inhibitors targeting the dimerization of SARS-CoV Mpro represents a potential therapeutic strategy. In this regard, we have compiled the literature reports highlighting the effect of mutations and N-terminal deletion of residues of SARS-CoV Mpro on its dimerization and, thus, catalytic activity. We believe that the present review will stimulate research in this less explored yet quite significant area. The effect of the COVID-19 epidemic and the possibility of future CoV outbreaks strongly emphasize the urgent need for the design and development of potent antiviral agents against CoV infections.


Assuntos
Betacoronavirus/enzimologia , Infecções por Coronavirus/tratamento farmacológico , Cisteína Endopeptidases/metabolismo , Pneumonia Viral/tratamento farmacológico , Inibidores de Proteases/farmacologia , Multimerização Proteica/efeitos dos fármacos , Proteínas não Estruturais Virais/metabolismo , Antivirais/farmacologia , Betacoronavirus/química , Betacoronavirus/efeitos dos fármacos , Betacoronavirus/genética , Infecções por Coronavirus/virologia , Cisteína Endopeptidases/química , Cisteína Endopeptidases/genética , Descoberta de Drogas , Humanos , Modelos Moleculares , Terapia de Alvo Molecular , Mutação/efeitos dos fármacos , Pandemias , Peptídeos/farmacologia , Pneumonia Viral/virologia , Conformação Proteica/efeitos dos fármacos , Proteínas não Estruturais Virais/antagonistas & inibidores , Proteínas não Estruturais Virais/química , Proteínas não Estruturais Virais/genética
20.
Arch Biochem Biophys ; 687: 108388, 2020 07 15.
Artigo em Inglês | MEDLINE | ID: mdl-32343975

RESUMO

The active sites of metalloproteins may be mimicked by designing peptides that bind to their respective metal ions. Studying the binding of protein ligands to metal ions along with the associated structural changes is important in understanding metal uptake, transport and electron transfer functions of proteins. Copper-binding metalloprotein azurin is a 128-residue electron transfer protein with a redox-active copper cofactor. Here, we report the copper-binding associated spectroscopic and structural properties of peptide loops (11 and 13 residues) from the copper-binding site of azurin. These peptides develop a ß-turn upon copper-binding with a 1:1 Cu2+:peptide stoichiometry as seen in circular dichroism and exhibit electronic transitions centered at 340 nm and 540 nm. Further addition of copper develops a helical feature along with a shift in the absorption maxima to ~360 nm and ~580 nm at 2:1 Cu2+:peptide stoichiometry, indicating stoichiometric dependence of copper-binding geometry. Mass spectrometry indicates the copper-binding to cysteine, histidine and methionine in the peptide with 1:1 stoichiometry, and interestingly, dimerization through a disulfide linkage at 2:1 stoichiometry, as observed previously for denatured azurin. Fluorescence quenching studies on peptides with tryptophan further confirm the copper-binding induced changes in the two peptides are bi-phasic.


Assuntos
Azurina/metabolismo , Cobre/metabolismo , Fragmentos de Peptídeos/metabolismo , Conformação Proteica/efeitos dos fármacos , Azurina/química , Domínio Catalítico , Cobre/química , Fluorescência , Transferência Ressonante de Energia de Fluorescência , Fragmentos de Peptídeos/química , Ligação Proteica , Espectrometria de Massas por Ionização por Electrospray , Triptofano/química
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