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1.
Chemosphere ; 239: 124769, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31526997

RESUMO

In this study, Cerium chloride-induced conformational changes of Bovine Liver Catalase (BLC) has been investigated by molecular docking and further supported by various biophysical techniques. The temporal change of catalytic activity of BLC has also been studied in presence of Ce(III) with different buffer solution in vitro at 25 °C. The differential binding of Ce(III) to BLC observed by simulation study was well supported by the differential regulation of BLC activity in different buffers. After 1 h of incubation with CeCl3, the reduction in activity of BLC was maximum in MOPS, HEPES and Tris buffer, whereas no change in activity was noticed in phosphate buffer. Isothermal Titration Calorimetric (ITC) study also supports the differential binding of Ce(III) to BLC in different buffers. Ce(III)-induced conformational transition in BLC was followed as a function of concentration. Nevertheless, with 24 h incubation of CeCl3 the activity of BLC was highest with higher molar concentration of CeCl3 suggesting the conformational stability of BLC in presence of Ce(III). The compromised activity of BLC in response to Ce(III) is due to the induced conformational change and the degree of change in secondary conformation of BLC was maximum in MOPS, HEPES and Tris and least in phosphate buffer. Therefore, the reduced activity of BLC is controlled by the direct interaction of Ce(III) in the active site of BLC in Tris buffer or indirect interaction of Ce(III) in the non-active site of BLC in MOPS and HEPES buffer.


Assuntos
Catalase/química , Catalase/metabolismo , Cério/química , Fígado/enzimologia , Animais , Tampões (Química) , Calorimetria , Domínio Catalítico , Bovinos , Cério/metabolismo , Cloretos/química , Simulação de Acoplamento Molecular , Conformação Proteica
2.
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
3.
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
4.
Biosci Biotechnol Biochem ; 84(1): 63-75, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31462179

RESUMO

A natural isoquinoline alkaloid, berberine, has been known to exhibit anti-tumor activity in various cancer cells via inducing cell cycle arrest. However, it has not been investigated whether berberine and its analogs inhibit the growth of rhabdomyosarcoma (RMS), which is the most frequent soft tissue tumor in children. The present study examined the anti-tumor effects of berberine and palmatine on expansions of three human embryonal RMS cell lines; ERMS1, KYM1, and RD. Intracellular incorporation of berberine was relatively higher than that of palmatine in every RMS cell line. Berberine significantly inhibited the cell cycle of all RMS cells at G1 phase. On the other hand, palmatine only suppressed the growth of RD cells. Both of berberine and palmatine strongly inhibited the growth of tumorsphere of RD cells in three-dimensional culture. These results indicate that berberine derivatives have the potential of anti-tumor drugs for RMS therapy.Abbreviations: ARMS: alveolar rhabdomyosarcoma; ERMS: embryonal rhabdomyosarcoma; RMS: rhabdomyosarcoma.


Assuntos
Antineoplásicos/farmacologia , Alcaloides de Berberina/farmacologia , Berberina/farmacologia , Proliferação de Células/efeitos dos fármacos , Medicamentos de Ervas Chinesas/farmacologia , Rabdomiossarcoma Alveolar/patologia , Rabdomiossarcoma Embrionário/patologia , Antineoplásicos/química , Berberina/análogos & derivados , Berberina/química , Alcaloides de Berberina/química , Linhagem Celular Tumoral , Ciclina D1/genética , Inibidor de Quinase Dependente de Ciclina p57/genética , Avaliação Pré-Clínica de Medicamentos/métodos , Medicamentos de Ervas Chinesas/química , Pontos de Checagem da Fase G1 do Ciclo Celular/efeitos dos fármacos , Expressão Gênica/efeitos dos fármacos , Regulação Neoplásica da Expressão Gênica , Humanos , Antígeno Ki-67/genética , Conformação Molecular , Simulação de Acoplamento Molecular , Phellodendron/química , Rabdomiossarcoma Alveolar/metabolismo , Rabdomiossarcoma Embrionário/metabolismo
5.
J Enzyme Inhib Med Chem ; 35(1): 72-84, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31682465

RESUMO

Fibroblast growth-factor receptor (FGFR) is a potential target for cancer therapy. We designed three novel series of FGFR1 inhibitors bearing indazole, benzothiazole, and 1H-1,2,4-triazole scaffold via fragment-based virtual screening. All the newly synthesised compounds were evaluated in vitro for their inhibitory activities against FGFR1. Compound 9d bearing an indazole scaffold was first identified as a hit compound, with excellent kinase inhibitory activity (IC50 = 15.0 nM) and modest anti-proliferative activity (IC50 = 785.8 nM). Through two rounds of optimisation, the indazole derivative 9 u stood out as the most potent FGFR1 inhibitors with the best enzyme inhibitory activity (IC50 = 3.3 nM) and cellular activity (IC50 = 468.2 nM). Moreover, 9 u also exhibited good kinase selectivity. In addition, molecular docking study was performed to investigate the binding mode between target compounds and FGFR1.


Assuntos
Antineoplásicos/farmacologia , Benzotiazóis/farmacologia , Desenho de Drogas , Indazóis/farmacologia , Inibidores de Proteínas Quinases/farmacologia , Receptor Tipo 1 de Fator de Crescimento de Fibroblastos/antagonistas & inibidores , Triazóis/farmacologia , Antineoplásicos/síntese química , Antineoplásicos/química , Benzotiazóis/síntese química , Benzotiazóis/química , Linhagem Celular Tumoral , Proliferação de Células/efeitos dos fármacos , Relação Dose-Resposta a Droga , Ensaios de Seleção de Medicamentos Antitumorais , Humanos , Indazóis/síntese química , Indazóis/química , Simulação de Acoplamento Molecular , Estrutura Molecular , Inibidores de Proteínas Quinases/síntese química , Inibidores de Proteínas Quinases/química , Receptor Tipo 1 de Fator de Crescimento de Fibroblastos/metabolismo , Relação Estrutura-Atividade , Triazóis/síntese química , Triazóis/química
6.
J Enzyme Inhib Med Chem ; 35(1): 199-210, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31752556

RESUMO

Previous reports have validated the glycogen synthase kinase-3 (GSK-3) as a druggable target against the human protozoan parasite Leishmania. This prompted us to search for new leishmanicidal scaffolds as inhibitors of this enzyme from our in-house library of human GSK-3ß inhibitors, as well as from the Leishbox collection of leishmanicidal compounds developed by GlaxoSmithKline. As a result, new leishmanicidal inhibitors acting on Leishmania GSK-3 at micromolar concentrations were found. These inhibitors belong to six different chemical classes (thiadiazolidindione, halomethylketone, maleimide, benzoimidazole, N-phenylpyrimidine-2-amine and oxadiazole). In addition, the binding mode of the most active compounds into Leishmania GSK-3 was approached using computational tools. On the whole, we have uncovered new chemical scaffolds with an appealing prospective in the development and use of Leishmania GSK-3 inhibitors against this infectious protozoan.


Assuntos
Antiprotozoários/farmacologia , Descoberta de Drogas , Quinase 3 da Glicogênio Sintase/antagonistas & inibidores , Leishmania/efeitos dos fármacos , Inibidores de Proteínas Quinases/farmacologia , Antiprotozoários/síntese química , Antiprotozoários/química , Relação Dose-Resposta a Droga , Quinase 3 da Glicogênio Sintase/metabolismo , Humanos , Leishmania/citologia , Leishmania/enzimologia , Simulação de Acoplamento Molecular , Estrutura Molecular , Testes de Sensibilidade Parasitária , Inibidores de Proteínas Quinases/síntese química , Inibidores de Proteínas Quinases/química , Relação Estrutura-Atividade
7.
J Enzyme Inhib Med Chem ; 35(1): 235-244, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31760818

RESUMO

Cyclin-dependent kinase 2 (CDK2) is the family of Ser/Thr protein kinases that has emerged as a highly selective with low toxic cancer therapy target. A multistage virtual screening method combined by SVM, protein-ligand interaction fingerprints (PLIF) pharmacophore and docking was utilised for screening the CDK2 inhibitors. The evaluation of the validation set indicated that this method can be used to screen large chemical databases because it has a high hit-rate and enrichment factor (80.1% and 332.83 respectively). Six compounds were screened out from NCI, Enamine and Pubchem database. After molecular dynamics and binding free energy calculation, two compounds had great potential as novel CDK2 inhibitors and they also showed selective inhibition against CDK2 in the kinase activity assay.


Assuntos
Antineoplásicos/análise , Antineoplásicos/farmacologia , Quinase 2 Dependente de Ciclina/antagonistas & inibidores , Simulação de Acoplamento Molecular , Inibidores de Proteínas Quinases/análise , Inibidores de Proteínas Quinases/farmacologia , Máquina de Vetores de Suporte , Células A549 , Antineoplásicos/química , Proliferação de Células/efeitos dos fármacos , Quinase 2 Dependente de Ciclina/metabolismo , Relação Dose-Resposta a Droga , Avaliação Pré-Clínica de Medicamentos , Ensaios de Seleção de Medicamentos Antitumorais , Células HCT116 , Humanos , Estrutura Molecular , Inibidores de Proteínas Quinases/química , Relação Estrutura-Atividade
8.
J Enzyme Inhib Med Chem ; 35(1): 298-305, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31809607

RESUMO

Pursuing on our efforts toward searching for efficient hCA IX and hCA XII inhibitors, herein we report the design and synthesis of new sets of benzofuran-based sulphonamides (4a,b, 5a,b, 9a-c, and 10a-d), featuring the zinc anchoring benzenesulfonamide moiety linked to a benzofuran tail via a hydrazine or hydrazide linker. All the target benzofurans were examined for their inhibitory activities toward isoforms hCA I, II, IX, and XII. The target tumour-associated hCA IX and XII isoforms were efficiently inhibited with KIs spanning in ranges 10.0-97.5 and 10.1-71.8 nM, respectively. Interestingly, arylsulfonehydrazones 9 displayed the best selectivity toward hCA IX and XII over hCA I (SIs: 39.4-250.3 and 26.0-149.9, respectively), and over hCA II (SIs: 19.6-57.1 and 13.0-34.2, respectively). Furthermore, the target benzofurans were assessed for their anti-proliferative activity, according to US-NCI protocol, toward a panel of sixty cancer cell lines. Only benzofurans 5b and 10b possessed selective and moderate growth inhibitory activity toward certain cancer cell lines.


Assuntos
Antineoplásicos/farmacologia , Benzofuranos/farmacologia , Anidrase Carbônica IX/antagonistas & inibidores , Inibidores da Anidrase Carbônica/farmacologia , Anidrases Carbônicas/metabolismo , Sulfonamidas/farmacologia , Antígenos de Neoplasias/metabolismo , Antineoplásicos/síntese química , Antineoplásicos/química , Benzofuranos/química , Anidrase Carbônica IX/metabolismo , Inibidores da Anidrase Carbônica/síntese química , Inibidores da Anidrase Carbônica/química , Linhagem Celular Tumoral , Proliferação de Células/efeitos dos fármacos , Relação Dose-Resposta a Droga , Ensaios de Seleção de Medicamentos Antitumorais , Humanos , Simulação de Acoplamento Molecular , Estrutura Molecular , Relação Estrutura-Atividade , Sulfonamidas/síntese química , Sulfonamidas/química
9.
J Enzyme Inhib Med Chem ; 35(1): 311-324, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31809612

RESUMO

Hybridization of reported weakly active antiproliferative hit 5-amino-4-pyrimidinol derivative with 2-anilino-4-phenoxypyrimidines suggests a series of 2,5-diamino-4-pyrimidinol derivatives as potential antiproliferative agents. Few compounds belonging to the proposed series were reported as CSF1R/DAPK1 inhibitors as anti-tauopathies. However, the correlation between CSF1R/DAPK1 signalling pathways and cancer progression provides motives to reprofile them against cancer therapy. The compounds were synthesised, characterized, and evaluated against M-NFS-60 cells and a kinase panel which bolstered predictions of their antiproliferative activity and suggested the involvement of diverse molecular targets. Compound 6e, the most potent in the series, showed prominent broad-spectrum antiproliferative activity inhibiting the growth of hematological, NSCLC, colon, CNS, melanoma, ovarian, renal, prostate and breast cancers by 84.1, 52.79, 72.15, 66.34, 66.48, 51.55, 55.95, 61.85, and 60.87%, respectively. Additionally, it elicited an IC50 value of 1.97 µM against M-NFS-60 cells and good GIT absorption with Pe value of 19.0 ± 1.1 × 10-6 cm/s (PAMPA-GIT). Molecular docking study for 6e with CSF1R and DAPK1 was done to help to understand the binding mode with both kinases. Collectively, compound 6e could be a potential lead compound for further development of anticancer therapies.


Assuntos
Antineoplásicos/farmacologia , Proteínas Quinases Associadas com Morte Celular/antagonistas & inibidores , Inibidores de Proteínas Quinases/farmacologia , Pirimidinas/farmacologia , Receptores de Fator Estimulador das Colônias de Granulócitos e Macrófagos/antagonistas & inibidores , Antineoplásicos/síntese química , Antineoplásicos/química , Linhagem Celular Tumoral , Proliferação de Células/efeitos dos fármacos , Proteínas Quinases Associadas com Morte Celular/metabolismo , Relação Dose-Resposta a Droga , Ensaios de Seleção de Medicamentos Antitumorais , Humanos , Simulação de Acoplamento Molecular , Estrutura Molecular , Inibidores de Proteínas Quinases/síntese química , Inibidores de Proteínas Quinases/química , Pirimidinas/síntese química , Pirimidinas/química , Receptores de Fator Estimulador das Colônias de Granulócitos e Macrófagos/metabolismo , Relação Estrutura-Atividade
10.
J Sci Food Agric ; 100(1): 315-324, 2020 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-31525262

RESUMO

BACKGROUND: In order to utilize tilapia skin gelatin hydrolysate protein, which is normally discarded as industrial waste in the process of fish manufacture, we study the in vivo and in vitro angiotensin-I-converting enzyme (ACE) inhibitory activity of the peptide Leu-Ser-Gly-Tyr-Gly-Pro (LSGYGP). The aim was to provide a pharmacological basis of the development of minimal side effects of ACE inhibitors by comparative analysis with captopril in molecular docking. RESULTS: This peptide from protein-rich wastes showed excellent ACE inhibitory activity (IC50  = 2.577 µmol L-1 ) and exhibited a mixed noncompetitive inhibitory pattern with Lineweaver-Burk plots. Furthermore, LSGYGP and captopril groups both showed significant decreases in blood pressure after 6 h and maintained good digestive stability over 4 h. Molecular bond interactions differentiate competitive captopril upon hydrogen bond interactions and Zn(II) interaction. The C-terminal Pro generates three interactions (hydrogen bonds, hydrophilic interactions and Van der Waals interactions) in the peptide and effectively interacts with the S1 and S2 pockets of ACE. CONCLUSION: LSGYGP, with an IC50 value of 2.577 µmol L-1 , has an antihypertensive effect in spontaneously hypertensive rats. Through comparison with captopril, this study revealed that LSGYGP may be a potential food-derived ACE inhibitory peptide and could act as a functional food ingredient to prevent hypertension. © 2019 Society of Chemical Industry.


Assuntos
Inibidores da Enzima Conversora de Angiotensina/química , Anti-Hipertensivos/química , Captopril/química , Hipertensão/tratamento farmacológico , Peptídeos/química , Sequência de Aminoácidos , Inibidores da Enzima Conversora de Angiotensina/administração & dosagem , Inibidores da Enzima Conversora de Angiotensina/metabolismo , Animais , Anti-Hipertensivos/administração & dosagem , Anti-Hipertensivos/metabolismo , Pressão Sanguínea/efeitos dos fármacos , Captopril/administração & dosagem , Ciclídeos , Digestão , Proteínas de Peixes/química , Trato Gastrointestinal/metabolismo , Humanos , Ligações de Hidrogênio , Interações Hidrofóbicas e Hidrofílicas , Hipertensão/metabolismo , Hipertensão/fisiopatologia , Cinética , Masculino , Simulação de Acoplamento Molecular , Peptídeos/metabolismo , Peptídeos/farmacologia , Peptidil Dipeptidase A/química , Peptidil Dipeptidase A/metabolismo , Hidrolisados de Proteína/química , Hidrolisados de Proteína/metabolismo , Ratos , Ratos Endogâmicos SHR
11.
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
12.
Zhongguo Zhong Yao Za Zhi ; 44(18): 4043-4047, 2019 Sep.
Artigo em Chinês | MEDLINE | ID: mdl-31872743

RESUMO

The purpose of this study was to investigate the effect of apigenin on UGT1 A1 enzyme activity and to predict the potential drug-drug interaction of apigenin in clinical use. First,on the basis of previous experiments,the binding targets and binding strength of apigenin to UGT1 A1 enzyme were predicted by computer molecular docking method. Then the inhibitory effect of apigenin on UGT1 A1 enzyme was evaluated by in vitro human liver microsomal incubation system. Molecular docking results showed that apigenin was docked into the active region of UGT1 A1 enzyme protein F,consistent with the active region of bilirubin docking,with moderate affinity. Apigenin flavone mother nucleus mainly interacted with amino acid residues ILE343 and VAL345 to form hydrophobic binding Pi-Alkyl. At the same time,the hydroxyl group on the mother nucleus and the amino acid residue LYS346 formed an additional hydrogen bond,which increased the binding of the molecule to the protein. These results suggested that the flavonoid mother nucleus structure had a special structure binding to the enzyme protein UGT1 A1,and the introduction of hydroxyl groups into the mother nucleus can increase the binding ability. In vitro inhibition experiments showed that apigenin had a moderate inhibitory effect on UGT1 A1 enzyme in a way of competitive inhibition,which was consistent with the results of molecular docking. The results of two experiments showed that apigenin was the substrate of UGT1 A1 enzyme,which could inhibit the activity of UGT1 A1 enzyme competitively,and there was a risk of drug interaction between apigenin and UGT1 A1 enzyme substrate in clinical use.


Assuntos
Apigenina/química , Bilirrubina/química , Interações de Medicamentos , Microssomos Hepáticos/efeitos dos fármacos , Simulação de Acoplamento Molecular , Glucuronosiltransferase/metabolismo , Humanos , Ligações de Hidrogênio
13.
Phys Chem Chem Phys ; 21(45): 25276-25289, 2019 Dec 07.
Artigo em Inglês | MEDLINE | ID: mdl-31701109

RESUMO

As a member of the bromodomain and extra terminal domain (BET) protein family, bromodomain-containing protein 4 (BRD4) is an epigenetic reader and can recognize acetylated lysine residues in histones. BRD4 has been regarded as an essential drug target for cancers, inflammatory diseases and acute heart failure, and therefore the discovery of potent BRD4 inhibitors with novel scaffolds is highly desirable. In this study, the crystalline water molecules in BRD4 involved in ligand binding were analyzed first, and the simulation results suggest that several conserved crystalline water molecules are quite essential to keep the stability of the crystalline water network and therefore they need to be reserved in structure-based drug design. Then, a docking-based virtual screening workflow with the consideration of the conserved crystalline water network in the binding pocket was utilized to identify the potential inhibitors of BRD4. The in vitro fluorescence resonance energy transfer (HTRF) binding assay illustrates that 4 hits have good inhibitory activity against BRD4 in the micromolar regime, including three compounds with IC50 values below 5 µM and one below 1 µM (0.37 µM). The structural analysis demonstrates that three active compounds possess novel scaffolds. Moreover, the interaction patterns between the hits and BRD4 were characterized by molecular dynamics simulations and binding free energy calculations, and then several suggestions for the further optimization of these hits were proposed.


Assuntos
Simulação de Acoplamento Molecular , Proteínas Nucleares/química , Fatores de Transcrição/química , Água/química , Proteínas de Ciclo Celular , Cristalização , Transferência Ressonante de Energia de Fluorescência , Humanos , Simulação de Dinâmica Molecular , Proteínas Nucleares/antagonistas & inibidores , Fatores de Transcrição/antagonistas & inibidores
14.
Sheng Wu Gong Cheng Xue Bao ; 35(10): 1819-1828, 2019 Oct 25.
Artigo em Chinês | MEDLINE | ID: mdl-31668031

RESUMO

We review major computational chemistry techniques applied in industrial enzyme studies, especially approaches intended for guiding enzyme engineering. These include molecular mechanics force field and molecular dynamics simulation, quantum mechanical and combined quantum mechanical/molecular mechanical approaches, electrostatic continuum models, molecular docking, etc. These approaches are essentially introduced from the following two angles for viewing: one is about the methods themselves, including the basic concepts, the primary computational results, and potential advantages and limitations; the other is about obtaining valuable information from the respective calculations to guide the design of mutants and mutant libraries.


Assuntos
Enzimas/metabolismo , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Engenharia de Proteínas , Teoria Quântica , Enzimas/química , Enzimas/genética , Proteínas Mutantes/química , Proteínas Mutantes/genética , Proteínas Mutantes/metabolismo , Eletricidade Estática
16.
Phys Chem Chem Phys ; 21(42): 23501-23513, 2019 Nov 14.
Artigo em Inglês | MEDLINE | ID: mdl-31617551

RESUMO

YIV-906 (formally PHY906, KD018) is a four-herb formulation that is currently being developed to improve the therapeutic index and ameliorate the side effects of many chemotherapeutic drugs including sorafenib, irinotecan, and capecitabine. However, as a promising anti-cancer adjuvant, the molecular mechanism of action of YIV-906 remains unrevealed due to its multi-component and multi-target features. Since YIV-906 has been shown to induce apoptosis and autophagy in cancer cells through modulating the negative regulators of ERK1/2, namely DUSPs, it is of great interest to elucidate the key components that cause the therapeutic effect of YIV-906. In this work, we investigated the mechanism of YIV-906 inhibiting DUSPs, using a broad spectrum of molecular modelling techniques, including molecular docking, molecular dynamics (MD) simulations, and binding free energy calculations. In total, MD simulations and binding free energy calculations were performed for 99 DUSP-ligand complexes. We found that some herbal components or their metabolites could inhibit DUSPs. Based on the docking scores and binding free energies, the sulfation and glucuronidation metabolites of the S ingredient in YIV-906 play a leading role in inhibiting DUSPs, although several original herbal chemicals with carboxyl groups from the P and Z ingredients also make contributions to this inhibitory effect. It is not a surprise that the electrostatic interaction plays the dominant role in the ligand binding process, given the fact that several charged residues reside in the binding pockets of DUSPs. Our MD simulation results demonstrate that the sulfate moieties and carboxyl moieties of the advantageous ligands from YIV-906 can occupy the enzymes' catalytic sites, mimicking the endogenous phosphate substrates of DUSPs. As such, the ligand binding can inhibit the association of DUSPs and ERK1/2, which in turn reduces the dephosphorylation of ERK1/2 and causes cell cycle arrest in the tumor. Our modelling study provides useful insights into the rational design of highly potent anti-cancer drugs targeting DUSPs. Finally, we have demonstrated that multi-scale molecular modelling techniques are able to elucidate molecular mechanisms involving complex molecular systems.


Assuntos
Antineoplásicos Fitogênicos/química , Medicamentos de Ervas Chinesas/química , Antineoplásicos Fitogênicos/metabolismo , Sítios de Ligação , Domínio Catalítico , Medicamentos de Ervas Chinesas/metabolismo , Fosfatases de Especificidade Dupla/antagonistas & inibidores , Fosfatases de Especificidade Dupla/metabolismo , Humanos , Ligantes , Proteína Quinase 3 Ativada por Mitógeno/química , Proteína Quinase 3 Ativada por Mitógeno/metabolismo , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Termodinâmica
17.
Zhongguo Zhong Yao Za Zhi ; 44(15): 3157-3161, 2019 Aug.
Artigo em Chinês | MEDLINE | ID: mdl-31602867

RESUMO

In order to study the interaction between Pterocephalus hookeri and bitter taste receptors,three-dimensional structural models of bitter taste receptors TAS2 R16,TAS2 R14 and TAS2 R13 were established by homology modeling in this paper. Maestro software was used for docking the chemical constituents of P. hookeri with bitter taste receptors. The results showed that 25 chemical components of P. hookeri can regulate three bitter taste receptors. And these components were mainly iridoid glycosides and phenolic acids.This research focused on the comprehensive application of homology modeling and molecular docking technology to explore the interaction between bitter chemical constituents of P. hookeri and bitter taste receptors. This study provided assistance in revealing pharmacodynamic basis of bitter Tibetan medicine at molecular level. It also provided new ideas and methods for the study of Tibetan medicine.


Assuntos
Caprifoliaceae/química , Medicina Tradicional Tibetana , Simulação de Acoplamento Molecular , Receptores Acoplados a Proteínas-G/metabolismo , Correlação de Dados , Humanos , Paladar
18.
Zhongguo Zhong Yao Za Zhi ; 44(17): 3637-3644, 2019 Sep.
Artigo em Chinês | MEDLINE | ID: mdl-31602935

RESUMO

The biopharmaceutics classification system( BCS) is a scientific framework or method for classifying drugs based on drug solubility and permeability,which can be used to provide drug bioavailability-absorption correlation analysis. Based on the characteristics of multi-component and multi-target of traditional Chinese medicine( TCM) as well as the concept,method and technology of BCS,the research group proposed biopharmaceutics classification system of Chinese materia medica( CMMBCS) and carried out research and data accumulation of classical prescriptions. Based on the previous research results,further development ideas under the CMMBCS concept and framework were further proposed in this study. In the course of research,the influence of the intermediate links of the complex interactions of the multi-component environment was omitted,and the component absorption studies on the main clinical effects of prescription ingredients were directly concerned,or the components and data were reversely extracted from the aspects of metabolism,pharmacodynamic pathways and absorption principles. Studies were conducted from two aspects( single component and compound prescription) to comprehensively evaluate the absorption properties of TCM compound. In the research path,the different ways in which Chinese medicine could exert its efficacy were fully considered,and CMMBCS classification and establishment rules were clarified mainly by focusing on the absorption pathway into the blood. Specifically,the network pharmacology and molecular docking technology were used to screen the compound index components of TCM; the absorption rules were studied by the physiologically based pharmacokinetic models and the absorption parameters of CMMBCS were calculated by reverse reasoning. Then the CMMBCS classification of TCM prescription was corrected by studying the efficacy or absorption pathway. In this paper,the theoretical framework and research methodology of CMMBCS were systematically improved based on the establishment of CMMBCS basic theory,the supplementary of drug-oriented research ideas and the application of modern mature Chinese medicine methodology.


Assuntos
Biofarmácia/classificação , Medicamentos de Ervas Chinesas/classificação , Materia Medica/classificação , Simulação de Acoplamento Molecular
20.
Environ Sci Technol ; 53(21): 12706-12714, 2019 Nov 05.
Artigo em Inglês | MEDLINE | ID: mdl-31593449

RESUMO

Viral contamination of drinking water due to fecal contamination is difficult to detect and treat effectively, leading to frequent outbreaks worldwide. The purpose of this paper is to report on the molecular mechanism for unprecedented high virus removal from a practical sand filter. Sand filters functionalized using a water extract of Moringa oleifera (MO) seeds, functionalized sand (f-sand) filters, achieved a ∼7 log10 virus removal. These tests were conducted with MS2 bacteriophage, a recognized surrogate for pathogenic norovirus and rotavirus. We studied the molecular mechanism of this high removal since it can have important implications for sand filtration, the most common water treatment technology worldwide. Our data reveal that the virus removal activity of f-sand is due to the presence of a chitin-binding protein, M. oleifera chitin-binding protein (MoCBP) on f-sand. Standard column experiments were supported by proteomic analysis and molecular docking simulations. Our simulations show that MoCBP binds preferentially to MS2 capsid proteins demonstrating that specific molecular interactions are responsible for enhanced virus removal. In addition, we simplified the process of making f-sand and evinced how it could be regenerated using saline water. At present, no definitive solution exists for the challenge of treating fecally contaminated drinking and irrigation water for viruses without using technologies that demand high energy or chemical consumption. We propose functionalized sand (f-sand) filters as a highly effective, energy-efficient, and practical technology for virus removal applicable to both developing and developed countries.


Assuntos
Proteômica , Purificação da Água , Filtração , Levivirus , Simulação de Acoplamento Molecular , Dióxido de Silício
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