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1.
Int J Mol Sci ; 21(9)2020 Apr 28.
Artigo em Inglês | MEDLINE | ID: mdl-32353978

RESUMO

The novel coronavirus whose outbreak took place in December 2019 continues to spread at a rapid rate worldwide. In the absence of an effective vaccine, inhibitor repurposing or de novo drug design may offer a longer-term strategy to combat this and future infections due to similar viruses. Here, we report on detailed classical and mixed-solvent molecular dynamics simulations of the main protease (Mpro) enriched by evolutionary and stability analysis of the protein. The results were compared with those for a highly similar severe acute respiratory syndrome (SARS) Mpro protein. In spite of a high level of sequence similarity, the active sites in both proteins showed major differences in both shape and size, indicating that repurposing SARS drugs for COVID-19 may be futile. Furthermore, analysis of the binding site's conformational changes during the simulation time indicated its flexibility and plasticity, which dashes hopes for rapid and reliable drug design. Conversely, structural stability of the protein with respect to flexible loop mutations indicated that the virus' mutability will pose a further challenge to the rational design of small-molecule inhibitors. However, few residues contribute significantly to the protein stability and thus can be considered as key anchoring residues for Mpro inhibitor design.


Assuntos
Betacoronavirus/enzimologia , Cisteína Endopeptidases/química , Desenho de Fármacos , Inibidores de Proteases/farmacologia , Bibliotecas de Moléculas Pequenas , Proteínas não Estruturais Virais/antagonistas & inibidores , Proteínas não Estruturais Virais/química , Antivirais/farmacologia , Betacoronavirus/efeitos dos fármacos , Betacoronavirus/genética , Sítios de Ligação , Domínio Catalítico , Infecções por Coronavirus , Cristalografia por Raios X , Cisteína Endopeptidases/genética , Avaliação Pré-Clínica de Medicamentos , Evolução Molecular , Modelos Moleculares , Simulação de Dinâmica Molecular , Mutação , Pandemias , Pneumonia Viral , Vírus da SARS/enzimologia , Solventes , Termodinâmica , Proteínas não Estruturais Virais/genética
2.
Eur Rev Med Pharmacol Sci ; 24(8): 4529-4536, 2020 04.
Artigo em Inglês | MEDLINE | ID: mdl-32373991

RESUMO

OBJECTIVE: Currently, Coronavirus COVID-19 is spreading worldwide very rapidly and its control is very difficult because there is no effective vaccine or drugs available in markets. This virus can infect both animals and people and cause illnesses of the respiratory tract. WHO has declared Coronavirus as pandemic and the whole world is fighting against Coronavirus. Globally, more than 199,478 people have been diagnosed with COVID-19. As of March 18, 2020, more than 167 countries have been affected and more than 8000 deaths have been reported. The main country being affected is China followed by Italy, Iran, Spain, France, and the USA. MATERIALS AND METHODS: Since there are no effective drugs available against Coronavirus, we conducted virtual screening of phytochemicals to find novel compounds against this virus. Hence, we created a phytochemical library of 318 phytochemicals from 11 plants which have been reported as antiviral, antibacterial and antifungal activity. The phytochemical library was subjected to virtual screening against molecular targets; Main protease (Mpro) and Angiotensin-Converting Enzyme 2 (ACE2). RESULTS: Top 10 compounds were selected from each target which had better and significantly low binding energy as compared to the reference molecule. CONCLUSIONS: Based on the binding energy score, we suggest that these compounds can be tested against Coronavirus and used to develop effective antiviral drugs.


Assuntos
Betacoronavirus/efeitos dos fármacos , Infecções por Coronavirus/tratamento farmacológico , Simulação de Acoplamento Molecular , Compostos Fitoquímicos/farmacologia , Pneumonia Viral/tratamento farmacológico , Inibidores da Enzima Conversora de Angiotensina/farmacologia , Betacoronavirus/fisiologia , Cisteína Endopeptidases , Humanos , Pandemias , Peptidil Dipeptidase A , Relação Estrutura-Atividade , Proteínas não Estruturais Virais/antagonistas & inibidores , Internalização do Vírus/efeitos dos fármacos , Replicação Viral/efeitos dos fármacos
3.
Int J Mol Sci ; 21(10)2020 May 15.
Artigo em Inglês | MEDLINE | ID: mdl-32429099

RESUMO

Following the outbreak of novel severe acute respiratory syndrome (SARS)-coronavirus (CoV)2, the majority of nations are struggling with countermeasures to fight infection, prevent spread and improve patient survival. Considering that the pandemic is a recent event, no large clinical trials have been possible and since coronavirus specific drug are not yet available, there is no strong consensus on how to treat the coronavirus disease 2019 (COVID-19) associated viral pneumonia. Coronaviruses code for an important multifunctional enzyme named papain-like protease (PLP), that has many roles in pathogenesis. First, PLP is one of the two viral cysteine proteases, along with 3-chymotripsin-like protease, that is responsible for the production of the replicase proteins required for viral replication. Second, its intrinsic deubiquitinating and deISGylating activities serve to antagonize the host's immune response that would otherwise hinder infection. Both deubiquitinating and deISGylating functions involve the removal of the small regulatory polypeptides, ubiquitin and ISG15, respectively, from target proteins. Ubiquitin modifications can regulate the innate immune response by affecting regulatory proteins, either by altering their stability via the ubiquitin proteasome pathway or by directly regulating their activity. ISG15 is a ubiquitin-like modifier with pleiotropic effects, typically expressed during the host cell immune response. PLP inhibitors have been evaluated during past coronavirus epidemics, and have showed promising results as an antiviral therapy in vitro. In this review, we recapitulate the roles of PLPs in coronavirus infections, report a list of PLP inhibitors and suggest possible therapeutic strategies for COVID-19 treatment, using both clinical and preclinical drugs.


Assuntos
Betacoronavirus/enzimologia , Enzimas Desubiquitinantes/antagonistas & inibidores , Animais , Coronavirus/enzimologia , Infecções por Coronavirus/tratamento farmacológico , Cisteína Endopeptidases , Humanos , Pandemias , Pneumonia Viral/tratamento farmacológico , Proteínas não Estruturais Virais/antagonistas & inibidores
4.
Nature ; 581(7808): 252-255, 2020 05.
Artigo em Inglês | MEDLINE | ID: mdl-32415276

Assuntos
Antivirais/farmacologia , Betacoronavirus/química , Betacoronavirus/imunologia , Desenho de Fármacos , Proteínas Virais/antagonistas & inibidores , Proteínas Virais/química , Vacinas Virais , Monofosfato de Adenosina/análogos & derivados , Monofosfato de Adenosina/farmacologia , Monofosfato de Adenosina/uso terapêutico , Alanina/análogos & derivados , Alanina/farmacologia , Alanina/uso terapêutico , Animais , Antivirais/química , Azóis/farmacologia , Betacoronavirus/efeitos dos fármacos , Betacoronavirus/enzimologia , China , Infecções por Coronavirus/imunologia , Infecções por Coronavirus/prevenção & controle , Microscopia Crioeletrônica , Cristalização , Cristalografia por Raios X , Cisteína Endopeptidases/química , Cisteína Endopeptidases/metabolismo , Avaliação Pré-Clínica de Medicamentos , Alemanha , Ensaios de Triagem em Larga Escala , Humanos , Camundongos , National Institutes of Health (U.S.)/economia , National Institutes of Health (U.S.)/organização & administração , Compostos Organosselênicos/farmacologia , Peptidil Dipeptidase A/química , Peptidil Dipeptidase A/metabolismo , Inibidores de Proteases/farmacologia , RNA Replicase/antagonistas & inibidores , RNA Replicase/química , RNA Replicase/metabolismo , Glicoproteína da Espícula de Coronavírus/química , Glicoproteína da Espícula de Coronavírus/metabolismo , Síncrotrons , Fatores de Tempo , Reino Unido , Estados Unidos , Proteínas não Estruturais Virais/antagonistas & inibidores , Proteínas não Estruturais Virais/química , Proteínas não Estruturais Virais/metabolismo , Proteínas Virais/imunologia , Vacinas Virais/química , Vacinas Virais/imunologia
6.
Life Sci ; 252: 117652, 2020 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-32278693

RESUMO

AIMS: The severe acute respiratory syndrome coronavirus 2, better known as COVID-19 has become the current health concern to the entire world. Initially appeared in Wuhan, China around December 2019, it had spread to almost 187 countries due to its high contagious nature. Precautionary measures remain the sole obliging tactic to cease the person to person transmissions till any effective method of treatment or vaccine is developed. Amidst the pandemic, research and development of new molecule is labour-intensive and tedious process. Drug repurposing is the concept of identifying therapeutically potent molecule from the library of pre-existing molecules. MATERIALS AND METHODS: In the present study, 61 molecules that are already being used in clinics or under clinical scrutiny as antiviral agents are surveyed via docking study. Docking study was performed using Maestro interface (Schrödinger Suite, LLC, NY). KEY FINDINGS: Out of these 61 molecules, 37 molecules were found to interact with >2 protein structures of COVID-19. The docking results indicate that amongst the reported molecules, HIV protease inhibitors and RNA-dependent RNA polymerase inhibitors showed promising features of binding to COVID-19 enzyme. Along with these, Methisazone an inhibitor of protein synthesis, CGP42112A an angiotensin AT2 receptor agonist and ABT450 an inhibitor of the non-structural protein 3-4A might become convenient treatment option as well against COVID-19. SIGNIFICANCE: The drug repurposing approach provide an insight about the therapeutics that might be helpful in treating corona virus disease.


Assuntos
Antivirais/química , Betacoronavirus/enzimologia , Cisteína Endopeptidases/química , Reposicionamento de Medicamentos , Proteínas não Estruturais Virais/antagonistas & inibidores , Proteínas não Estruturais Virais/química , Simulação por Computador , Infecções por Coronavirus/tratamento farmacológico , Infecções por Coronavirus/virologia , Simulação de Acoplamento Molecular , Pandemias , Pneumonia Viral/tratamento farmacológico , Pneumonia Viral/virologia
7.
Science ; 368(6492): 779-782, 2020 05 15.
Artigo em Inglês | MEDLINE | ID: mdl-32277040

RESUMO

A novel coronavirus [severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2)] outbreak has caused a global coronavirus disease 2019 (COVID-19) pandemic, resulting in tens of thousands of infections and thousands of deaths worldwide. The RNA-dependent RNA polymerase [(RdRp), also named nsp12] is the central component of coronaviral replication and transcription machinery, and it appears to be a primary target for the antiviral drug remdesivir. We report the cryo-electron microscopy structure of COVID-19 virus full-length nsp12 in complex with cofactors nsp7 and nsp8 at 2.9-angstrom resolution. In addition to the conserved architecture of the polymerase core of the viral polymerase family, nsp12 possesses a newly identified ß-hairpin domain at its N terminus. A comparative analysis model shows how remdesivir binds to this polymerase. The structure provides a basis for the design of new antiviral therapeutics that target viral RdRp.


Assuntos
Betacoronavirus/enzimologia , RNA Replicase/química , RNA Replicase/ultraestrutura , Proteínas não Estruturais Virais/química , Proteínas não Estruturais Virais/ultraestrutura , Monofosfato de Adenosina/análogos & derivados , Monofosfato de Adenosina/metabolismo , Monofosfato de Adenosina/farmacologia , Alanina/análogos & derivados , Alanina/metabolismo , Alanina/farmacologia , Antivirais/metabolismo , Antivirais/farmacologia , Domínio Catalítico , Microscopia Crioeletrônica , Desenho de Fármacos , Modelos Moleculares , Conformação Proteica em Folha beta , Domínios Proteicos , RNA Replicase/antagonistas & inibidores , RNA Replicase/metabolismo , Proteínas não Estruturais Virais/antagonistas & inibidores , Proteínas não Estruturais Virais/metabolismo
8.
Mar Drugs ; 18(4)2020 Apr 23.
Artigo em Inglês | MEDLINE | ID: mdl-32340389

RESUMO

The current emergency due to the worldwide spread of the COVID-19 caused by the new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a great concern for global public health. Already in the past, the outbreak of severe acute respiratory syndrome (SARS) in 2003 and Middle Eastern respiratory syndrome (MERS) in 2012 demonstrates the potential of coronaviruses to cross-species borders and further underlines the importance of identifying new-targeted drugs. An ideal antiviral agent should target essential proteins involved in the lifecycle of SARS-CoV. Currently, some HIV protease inhibitors (i.e., Lopinavir) are proposed for the treatment of COVID-19, although their effectiveness has not yet been assessed. The main protease (Mpr) provides a highly validated pharmacological target for the discovery and design of inhibitors. We identified potent Mpr inhibitors employing computational techniques that entail the screening of a Marine Natural Product (MNP) library. MNP library was screened by a hyphenated pharmacophore model, and molecular docking approaches. Molecular dynamics and re-docking further confirmed the results obtained by structure-based techniques and allowed this study to highlight some crucial aspects. Seventeen potential SARS-CoV-2 Mpr inhibitors have been identified among the natural substances of marine origin. As these compounds were extensively validated by a consensus approach and by molecular dynamics, the likelihood that at least one of these compounds could be bioactive is excellent.


Assuntos
Antivirais/farmacologia , Betacoronavirus/enzimologia , Infecções por Coronavirus , Pandemias , Pneumonia Viral , Inibidores de Proteases/farmacologia , Proteínas não Estruturais Virais/antagonistas & inibidores , Antivirais/química , Antivirais/uso terapêutico , Betacoronavirus/efeitos dos fármacos , Produtos Biológicos/química , Produtos Biológicos/farmacologia , Produtos Biológicos/uso terapêutico , Infecções por Coronavirus/tratamento farmacológico , Infecções por Coronavirus/virologia , Cisteína Endopeptidases , Bases de Dados de Compostos Químicos , Humanos , Modelos Moleculares , Simulação de Acoplamento Molecular , Pneumonia Viral/tratamento farmacológico , Pneumonia Viral/virologia , Inibidores de Proteases/química , Inibidores de Proteases/uso terapêutico
9.
Comput Biol Chem ; 84: 107167, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31855781

RESUMO

BACKGROUND: Hepatitis C Virus (HCV) infection is a major public health concern across the globe. At present, direct-acting antivirals are the treatment of choice. However, the long-term effect of this therapy has yet to be ascertained. Previously, fluoroquinolones have been reported to inhibit HCV replication by targeting NS3 protein. Therefore, it is logical to hypothesize that the natural analogs of fluoroquinolones will exhibit NS3 inhibitory activity with substantially lesser side effects. METHOD: In this study, we tested the application of a recently devised integrated in-silico Cheminformatics-Molecular Docking approach to identify physicochemically similar natural analogs of fluoroquinolones from the available databases (Ambinter, Analyticon, Indofines, Specs, and TimTec). Molecular docking and ROC curve analyses were performed, using PatchDock and Graphpad software, respectively, to compare and analyze drug-protein interactions between active natural analogs, Fluoroquinolones, and HCV NS3 protein. RESULT: In our analysis, we were able to shortlist 18 active natural analogs, out of 10,399, that shared physicochemical properties with the template drugs (fluoroquinolones). These analogs showed comparable binding efficacy with fluoroquinolones in targeting 32 amino acids in the HCV NS3 active site that are crucial for NS3 activity. Our approach had around 80 % sensitivity and 70 % specificity in identifying physicochemically similar analogs of fluoroquinolones. CONCLUSION: Our current data suggest that our approach can be efficiently applied to identify putative HCV drug inhibitors that can be taken for in vitro testing. This approach can be applied to discover physicochemically similar analogs of virtually any drug, thus providing a speedy and inexpensive approach to complement drug discovery and design, which can tremendously economize on time and money spent on the screening of putative drugs.


Assuntos
Antivirais/metabolismo , Descoberta de Drogas/métodos , Inibidores Enzimáticos/metabolismo , Fluoroquinolonas/metabolismo , Proteínas não Estruturais Virais/antagonistas & inibidores , Antivirais/química , Domínio Catalítico , Quimioinformática , Inibidores Enzimáticos/química , Fluoroquinolonas/química , Hepacivirus/enzimologia , Simulação de Acoplamento Molecular , Ligação Proteica , Proteínas não Estruturais Virais/química , Proteínas não Estruturais Virais/metabolismo
10.
Comput Biol Chem ; 83: 107154, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31751885

RESUMO

Hepatitis C virus (HCV) NS3/4A protease is an attractive target for the development of antiviral therapy. However, the evolution of antiviral drug resistance is a major problem for treatment of HCV infected patients. Understanding of drug-resistance mechanisms at molecular level is therefore very important for the guidance of further design of antiviral drugs with high efficiency and specificity. Paritaprevir is a potent inhibitor against HCV NS3/4A protease genotype 1a. Unfortunately, this compound is highly susceptible to the substitution at D168 in the protease. In this work, molecular dynamics simulations of paritaprevir complexed with wild-type (WT) and two mutated strains (D168 N and D168Y) were carried out. Due to such mutations, the inhibitor-protein hydrogen bonding between them was weakened and the salt-bridge network among residues R123, R155 and D168 responsible for inhibitor binding was disrupted. Moreover, the per-residue free energy decomposition suggested that the main contributions from key residues such as Q80, V132, K136, G137 and R155 were lost in the D168 N/Y mutations. These lead to a lower binding affinity of paritaprevir for D168 N/Y variants of the HCV NS3/4A protease, consistent with the experimental data. This detailed information could be useful for further design of high potency anti-HCV NS3/4A inhibitors.


Assuntos
Antivirais/farmacologia , Peptídeos e Proteínas de Sinalização Intracelular/antagonistas & inibidores , Compostos Macrocíclicos/farmacologia , Simulação de Dinâmica Molecular , Mutação , Proteínas não Estruturais Virais/antagonistas & inibidores , Antivirais/química , Farmacorresistência Viral/efeitos dos fármacos , Ligação de Hidrogênio , Peptídeos e Proteínas de Sinalização Intracelular/genética , Peptídeos e Proteínas de Sinalização Intracelular/metabolismo , Compostos Macrocíclicos/química , Termodinâmica , Proteínas não Estruturais Virais/genética , Proteínas não Estruturais Virais/metabolismo
11.
PLoS Negl Trop Dis ; 13(11): e0007894, 2019 11.
Artigo em Inglês | MEDLINE | ID: mdl-31738758

RESUMO

Dengue is a mosquito-borne viral infection that has spread globally in recent years. Around half of the world's population, especially in the tropics and subtropics, is at risk of infection. Every year, 50-100 million clinical cases are reported, and more than 500,000 patients develop the symptoms of severe dengue infection: dengue haemorrhagic fever and dengue shock syndrome, which threaten life in Asia and Latin America. No antiviral drug for dengue is available. The dengue virus (DENV) non-structural protein 5 (NS5), which possesses the RNA-dependent RNA polymerase (RdRp) activity and is responsible for viral replication and transcription, is an attractive target for anti-dengue drug development. In the present study, 16,240 small-molecule compounds in a fragment library were screened for their capabilities to inhibit the DENV type 2 (DENV2) RdRp activities in vitro. Based on in cellulo antiviral and cytotoxity assays, we selected the compound RK-0404678 with the EC50 value of 6.0 µM for DENV2. Crystallographic analyses revealed two unique binding sites for RK-0404678 within the RdRp, which are conserved in flavivirus NS5 proteins. No resistant viruses emerged after nine rounds of serial passage of DENV2 in the presence of RK-0404678, suggesting the high genetic barrier of this compound to the emergence of a resistant virus. Collectively, RK-0404678 and its binding sites provide a new framework for antiviral drug development.


Assuntos
Antivirais/isolamento & purificação , Antivirais/farmacologia , Vírus da Dengue/efeitos dos fármacos , RNA Replicase/antagonistas & inibidores , Proteínas não Estruturais Virais/antagonistas & inibidores , Sítios de Ligação , Cristalografia por Raios X , Avaliação Pré-Clínica de Medicamentos , Testes de Sensibilidade Microbiana , Ligação Proteica , RNA Replicase/química , RNA Replicase/metabolismo , Proteínas não Estruturais Virais/química , Proteínas não Estruturais Virais/metabolismo
12.
Eur J Med Chem ; 184: 111747, 2019 Dec 15.
Artigo em Inglês | MEDLINE | ID: mdl-31604164

RESUMO

The present study reports on evaluation of anti-HCV activity and QSAR of certain arylidenethiazolidinone derivatives as potential inhibitors of HCV-NS5B polymerase. The pursued compounds involving, 5-aryliden-3-arylacetamidothiazolidin-2,4-diones 4-6(a-f), 5-arylidine-2-(N-arylacetamido)-iminothiazolidin-4-one (10) and their rigid counterparts 5-arylidinethiazolotriazines 13-15(a-f), were synthesized and their structures confirmed by spectral and elemental analyses. The results of NS5B polymerase inhibition assay revealed compound 4e, as the most active inhibitor (IC50 = 0.035 µM), which is four folds greater than that of the reference agent, VCH-759, (IC50 = 0.14 µM). Meanwhile, compounds 4b, 4c, 5a, and 5c, and 13b, 14e and 15c displayed equipotency to 2 folds higher activity than VCH-759 (IC50 values: 0.085, 0.14, 0.14, 0.10, 0.12, 0.09 and 0.07 µM, respectively). Assessment of the anti-HCV activity (GT1a) using human hepatoma cell line (Huh-7.5) illustrates superior activity of 4e (EC50 = 3.80 µM) relative to VCH-759 (EC50 = 5.29 µM). Cytotoxicity evaluation on, Transformed normal cell lines (Human Liver Epithelial-2, THLE-2 and Proximal Tubular Epithelial, RPTEC/TERT1), demonstrate enhanced safety profile of 4e (CC50 = 102.77, 161.37 µM, respectively) compared to VCH-759 (CC50 = 61.83, 81.28 µM, respectively). Molecular docking of the synthesized derivatives to NS5B polymerase allosteric site (PDB: 2HWH) showed similar binding modes to that of the co-crystallized ligand. Moreover, QSAR models were established for the studied thiazolidinones and thiazolotriazines to investigate the molecular characteristics contributing to the observed NS5B polymerase inhibition activity. The obtained results inspire further investigations of thiazolidinones and thiazolotriazine aiming at affording more potent, safe and orally active non-nucleoside NS5B polymerase inhibitors as anti-HCV drug candidates.


Assuntos
Antivirais/farmacologia , Hepacivirus/efeitos dos fármacos , Inibidores de Proteases/farmacologia , Relação Quantitativa Estrutura-Atividade , Proteínas não Estruturais Virais/antagonistas & inibidores , Antivirais/síntese química , Antivirais/química , Linhagem Celular , Sobrevivência Celular/efeitos dos fármacos , Relação Dose-Resposta a Droga , Hepacivirus/metabolismo , Humanos , Modelos Moleculares , Estrutura Molecular , Inibidores de Proteases/síntese química , Inibidores de Proteases/química , Tiazóis/síntese química , Tiazóis/química , Tiazóis/farmacologia , Tiazolidinas/síntese química , Tiazolidinas/química , Tiazolidinas/farmacologia , Triazinas/síntese química , Triazinas/química , Triazinas/farmacologia , Proteínas não Estruturais Virais/metabolismo
13.
Life Sci ; 238: 116958, 2019 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-31628915

RESUMO

AIM: To work on Hepatitis C Virus (HCV), one of the major causes of liver cirrhosis and hepatocellular carcinoma, polymerase of genotype 4a that have no solved structures deposited in the protein data bank (PDB) yet. Understanding the dynamics and testing some novel inhibitors are also covered. MATERIALS AND METHODS: Molecular Dynamics Simulation (MDS) is performed for a period of 1 µs on comparatively modeled then validated NS5b of subtype 4a. Following MDS analysis, molecular docking is performed to test the inhibitory performance of eight novels suggested guanosine derivatives using 181 different conformations of the protein model gathered during the MDS run after the equilibration period. KEY FINDINGS: The results yield that the eight modified, at position 2', GTP derivatives (fluorine, Hydroxyl, and sulphonyl oxydanyl) have binding energies comparable to the parent molecule, GTP. Besides, the eight suggested compounds have lower binding energies (and hence better in binding) compared to sofosbuvir (a drug approved by FDA in 2013 against HCV) and ribavirin (a wide range acting antiviral drug used before against HCV). SIGNIFICANCE: Combined molecular dynamics and molecular docking are able to test the hypothesis of HCV polymerase dynamics doesn't affect the nucleotides (or nucleotide inhibitors) binding to its active site. Despite the reported highly dynamic subtype 4a of HCV; all the nucleotide inhibitors under the study are able to, tightly, bind to NS5b of genotype 4a. This behavior is reported before for the Zika virus polymerase, as well.


Assuntos
Antivirais/química , Antivirais/farmacologia , Guanosina Trifosfato/química , Hepacivirus/efeitos dos fármacos , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Proteínas não Estruturais Virais/antagonistas & inibidores , Hepacivirus/classificação , Hepacivirus/genética , Humanos , Modelos Moleculares , Conformação Proteica , Proteínas não Estruturais Virais/genética , Proteínas não Estruturais Virais/metabolismo
14.
Gastroenterology ; 157(6): 1506-1517.e1, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-31401140

RESUMO

BACKGROUND & AIMS: Treatment options are limited for patients with hepatitis C (HCV) infection with treatment failure after sofosbuvir plus an NS5A inhibitor. There are some data for the efficacy of glecaprevir/pibrentasvir (G/P) in these patients. We performed a randomized trial of the safety and efficacy of 12 and 16 weeks of G/P, with or without ribavirin, in patients with HCV genotype 1 infection with treatment failure after sofosbuvir and an NS5A inhibitor. METHODS: We performed a phase 3b, open-label study of patients with chronic HCV genotype 1 infection who received previous treatment with sofosbuvir plus an NS5A inhibitor. Patients without cirrhosis were randomly assigned to groups that received G/P for 12 weeks (n = 78, group A) or 16 weeks (n = 49, group B). Patients with compensated cirrhosis were randomly assigned to groups that received G/P and ribavirin for 12 weeks (n = 21, group C) or G/P for 16 weeks (n = 29, group D). The primary end point was a sustained virologic response 12 weeks after treatment. Samples collected at baseline and at time of treatment failure were sequenced for resistance-associated substitutions in NS3 and NS5A. RESULTS: Of the 177 patients in the 4 groups, 81% were men, 79% had HCV genotype 1a infection, and 44% were black. Proportions of patients with sustained virologic response 12 weeks after treatment in groups A, B, C, and D were 90%, 94%, 86%, and 97%, respectively. The treatment failed in 13 (7.3%) patients with HCV genotype 1a infection, 6 (7.9%) in group A, 3 (6.1%) in group B, 3 (6.1%) in group C (6.1%), and 1 (3.4%) in group D. Most patients had baseline resistance-associated substitutions in NS5A. Treatment-emergent resistance-associated substitutions in NS3 and NS5A were observed in 9 and 10 patients with treatment failure, respectively. G/P was well tolerated. Ribavirin increased adverse events but did not increase efficacy. CONCLUSIONS: In a randomized study of patients with chronic HCV genotype 1 infection who received previous treatment with sofosbuvir plus an NS5A inhibitor, 16 weeks treatment with G/P produced sustained virologic response 12 weeks after treatment in >90% of patients, including those with compensated cirrhosis. ClinicalTrials.gov, Number: NCT03092375.


Assuntos
Antivirais/uso terapêutico , Hepacivirus/genética , Hepatite C Crônica/tratamento farmacológico , Adulto , Idoso , Idoso de 80 Anos ou mais , Antivirais/farmacologia , Benzimidazóis/farmacologia , Benzimidazóis/uso terapêutico , Combinação de Medicamentos , Farmacorresistência Viral Múltipla/genética , Quimioterapia Combinada , Feminino , Genótipo , Hepacivirus/isolamento & purificação , Hepatite C Crônica/virologia , Humanos , Masculino , Pessoa de Meia-Idade , Pirrolidinas/farmacologia , Pirrolidinas/uso terapêutico , Quinoxalinas/farmacologia , Quinoxalinas/uso terapêutico , Ribavirina/farmacologia , Ribavirina/uso terapêutico , Sofosbuvir/farmacologia , Sofosbuvir/uso terapêutico , Sulfonamidas/farmacologia , Sulfonamidas/uso terapêutico , Resposta Viral Sustentada , Falha de Tratamento , Proteínas não Estruturais Virais/antagonistas & inibidores , Proteínas não Estruturais Virais/genética
15.
Asian Pac J Cancer Prev ; 20(8): 2311-2317, 2019 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-31450900

RESUMO

Background: Even with the fantastic successes of direct-acting antivirals (DAA) in the treatment of Hepatitis C Virus (HCV) infection, natural drug resistance remains a challenging obstacle for their impacts. The data regarding protease inhibitors (PIs) resistance in Iran population are limited. The aim of this study was to investigate the variations in NS3 protease of HCV from non-responder patients. Methods: In this cross-sectional study, 14 HCV infected patients with genotype 1(N=5) and 3(N=9) who have not responded to Interferon-related regime were enrolled from Liver Clinic, Shiraz. The NS3 protease region was amplified by Nested-PCR followed by product gel extraction. Besides, some amplified protease regions were cloned into a cloning vector to improve the sensitivity of mutation detection. Both crude and cloned sequences were then introduced into sequencing. The obtained sequences were compared with the NS3 reference sequences and analyzed by Geno2pheno available software to find possible substitutions. In the end, the phylogenetic tree was constructed. Results: Among variations responsible for PIs resistance, only one out of 14 (7%) sample who was infected with genotype 1a, harbored R117C+N174S double mutation, which causes reduced susceptibility to Telaprevir. Any another resistance mutation was not found among the studied population. The most frequent substitutions were determined as I52M(N=9), S102A(N=9), S166A(8) and V170I(8) for genotype 3a, and F147S/A(4) for genotype 1. However, some uncharacterized substitutions on scored position, including I132L(N=1), I170V(N=3) and N174S(N=2) were also determined among sequences. Phylogenetic analysis demonstrated that the protease region has enough power to correctly classify enrolled samples into relevant clusters on the tree. There were 2, 3 and 9 cases of sub-genotypes 1a, 1b, and 3a, respectively. Conclusion: A low frequency of PIs resistance mutations in our HCV infected population is a hopeful point of starting these drugs in HCV infected patients.


Assuntos
Farmacorresistência Viral/genética , Hepacivirus/efeitos dos fármacos , Hepatite C/tratamento farmacológico , Mutação , Inibidores de Proteases/farmacologia , Proteínas não Estruturais Virais/antagonistas & inibidores , Proteínas não Estruturais Virais/genética , Adulto , Idoso , Substituição de Aminoácidos , Antivirais/farmacologia , Estudos Transversais , Feminino , Seguimentos , Hepacivirus/enzimologia , Hepacivirus/genética , Hepatite C/virologia , Humanos , Masculino , Pessoa de Meia-Idade , Filogenia
16.
Nat Commun ; 10(1): 3468, 2019 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-31371704

RESUMO

Targeted protein degradation is a promising drug development paradigm. Here we leverage this strategy to develop a new class of small molecule antivirals that induce proteasomal degradation of viral proteins. Telaprevir, a reversible-covalent inhibitor that binds to the hepatitis C virus (HCV) protease active site is conjugated to ligands that recruit the CRL4CRBN ligase complex, yielding compounds that can both inhibit and induce the degradation of the HCV NS3/4A protease. An optimized degrader, DGY-08-097, potently inhibits HCV in a cellular infection model, and we demonstrate that protein degradation contributes to its antiviral activity. Finally, we show that this new class of antiviral agents can overcome viral variants that confer resistance to traditional enzymatic inhibitors such as telaprevir. Overall, our work provides proof-of-concept that targeted protein degradation may provide a new paradigm for the development of antivirals with superior resistance profiles.


Assuntos
Antivirais/farmacologia , Farmacorresistência Viral/efeitos dos fármacos , Peptídeos e Proteínas de Sinalização Intracelular/antagonistas & inibidores , Inibidores de Proteases/farmacologia , Proteínas não Estruturais Virais/antagonistas & inibidores , Proteínas Adaptadoras de Transdução de Sinal/genética , Proteínas Adaptadoras de Transdução de Sinal/metabolismo , Antivirais/química , Linhagem Celular Tumoral , Desenho de Fármacos , Farmacorresistência Viral/genética , Técnicas de Silenciamento de Genes , Células HEK293 , Hepacivirus/efeitos dos fármacos , Hepacivirus/metabolismo , Hepatite C/tratamento farmacológico , Hepatite C/genética , Hepatite C/virologia , Humanos , Peptídeos e Proteínas de Sinalização Intracelular/metabolismo , Ligantes , Modelos Moleculares , Oligopeptídeos/química , Oligopeptídeos/farmacologia , Estudo de Prova de Conceito , Inibidores de Proteases/química , Proteólise/efeitos dos fármacos , Ubiquitina-Proteína Ligases/metabolismo , Proteínas não Estruturais Virais/metabolismo
17.
Curr Pharm Des ; 25(12): 1392-1401, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31258065

RESUMO

BACKGROUND: The recent Nipah virus (NiV) outbreak in India has caused a state of chaos, with potential to become the next international pandemic. There is still a great deal to learn about NiV for the development of a potent treatment against it. The NiV non-structural proteins play important roles in the lifecycle of the virus, with the RNA-dependent RNA-polymerase (RdRp) being a vital component in viral replication. In this study, we not only provide a comprehensive overview of all the literature concerning NiV, we also propose a model of the NiV RdRp and screen for potential inhibitors of the viral enzyme. METHODS: In this study, computational tools were utilized in the design of a NiV RdRp homology model. The active site of RdRp was then identified and potential inhibitors of the protein were discovered with the use of pharmacophore-based screening. RESULTS: Ramachandran plot analysis revealed a favourable model. Upon binding of nucleoside analog, 4'- Azidocytidine, active site residues Trp1714 and Ser1713 took part in stabilizing hydrogen bonds, while Thr1716, Ser1478, Ser1476 and Glu1465 contributed to hydrophobic interactions. Pharmacophore based screening yielded 18 hits, of which ZINC00085930 demonstrated the most optimal binding energy (-8.1 kcal/mol), validating its use for further analysis as an inhibitor of NiV. CONCLUSION: In this study we provide a critical guide, elucidating on the in silico requirements of the drug design and discovery process against NiV. This material lays a foundation for future research into the design and development of drugs that inhibit NiV.


Assuntos
Antivirais/farmacologia , Vírus Nipah/enzimologia , RNA Replicase/antagonistas & inibidores , Proteínas não Estruturais Virais/antagonistas & inibidores , Domínio Catalítico , Desenho de Fármacos , Vírus Nipah/patogenicidade , Vírus Nipah/fisiologia , Replicação Viral
18.
Biomed Chromatogr ; 33(11): e4644, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31276615

RESUMO

Telaprevir is a potent, selective, peptidomimetic inhibitor of the hepatitis C virus (HCV) NS3-4A serine protease. it is used for the treatment of HCV infection in combination with peginterferon alfa and ribavirin. In the present work, the E-Z isomerization process of telaprevir in solution was revealed by online HPLC-DAD (diode array detector)-MS, variable-temperature and variable-gradient experiments. The molecular geometry information of the two isomers was established by molecular mechanics calculations, and good correlation between the two isomers' UV-vis spectra and their molecular geometry information was also discovered. In addition, it was revealed by molecular docking that the two isomers have different affinities to HCV NS3•4A protease, and the Z isomer, the minor form of telaprevir in solution, is the more effective inhibitor of HCV NS3•4A protease. The investigation can provide more structure information about telaprevir in solution and in the binding process of HCV NS3•4A protease.


Assuntos
Antivirais/química , Antivirais/metabolismo , Cromatografia Líquida de Alta Pressão/métodos , Oligopeptídeos/química , Oligopeptídeos/metabolismo , Isomerismo , Espectrometria de Massas , Simulação de Acoplamento Molecular , Serina Proteases/química , Serina Proteases/metabolismo , Proteínas não Estruturais Virais/antagonistas & inibidores , Proteínas não Estruturais Virais/química , Proteínas não Estruturais Virais/metabolismo
19.
Eur J Med Chem ; 180: 536-545, 2019 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-31344613

RESUMO

Zika virus (ZIKV) infection recently resulted in an international health emergency the Americas in and despite its high profile there is currently no approved treatment for ZIKV infection with millions of people being at risk. ZIKV is a member of Flaviviridae family which includes prominent members such as dengue virus (DENV) and West Nile virus (WNV). One of the best validated targets for developing anti-flaviviral treatment for DENV and WNV infection is the NS2B/NS3 protease. However the inhibitors reported to date have shown limited promise for further clinical development largely due to poor cellular activity. Prompted by the conserved nature of the viral NS2B/NS3 protease across flaviviruses, we envisaged that small molecule inhibitors of the ZIKVpro may be developed by applying rational design on previously reported scaffolds with demonstrated activity against other flaviviral proteases. Starting with an earlier WNVpro hit we performed a scaffold hopping exercise and discovered that certain carbazole derivatives bearing amidine groups possessed submicromolar potency and significant cellular activity against ZIKV. We successfully addressed various issues with the synthesis of novel N-substituted carbazole-based amidines thus permitting a targeted SAR campaign. The in vitro biochemical and cell-based inhibitory profiles exhibited by the lead molecule described in this work (ZIKVpro IC50 0.52 µM, EC50 1.25 µM), is among the best reported to date. Furthermore, these molecules possess capacity for further optimization of pharmacokinetics and may evolve to broad spectrum flaviviral protease inhibitors.


Assuntos
Antivirais/farmacologia , Carbazóis/farmacologia , Inibidores de Proteases/farmacologia , Proteínas não Estruturais Virais/antagonistas & inibidores , Zika virus/efeitos dos fármacos , Zika virus/enzimologia , Antivirais/química , Carbazóis/química , Linhagem Celular Tumoral , Sobrevivência Celular/efeitos dos fármacos , Relação Dose-Resposta a Droga , Humanos , Testes de Sensibilidade Microbiana , Modelos Moleculares , Estrutura Molecular , Inibidores de Proteases/química , RNA Helicases/antagonistas & inibidores , RNA Helicases/metabolismo , Serina Endopeptidases/metabolismo , Relação Estrutura-Atividade , Proteínas não Estruturais Virais/metabolismo
20.
Food Funct ; 10(6): 3758-3767, 2019 Jun 19.
Artigo em Inglês | MEDLINE | ID: mdl-31179460

RESUMO

Hepatitis C virus (HCV) is the main agent responsible for chronic liver disease. Recent advances in anti-HCV treatment strategies have significantly increased the viral clearance rate (>90%). However, sustained antiviral responses vary in different cohorts, and high costs limit the broad use of direct-acting antivirals (DAAs). The goal of this study is to evaluate the inhibitory ability of well characterized (LC-QTOF-MS/MS) aqueous extracts obtained from edible mushrooms (Agaricus bisporus) to diminish HCV viral replication. Our data have demonstrated an in vitro inhibitory effect of A. bisporus extracts on NS3/4A protease and HCV replication. Fractionation by ultra-filtration and sequential liquid-liquid extraction showed that the compounds responsible for the inhibition are water-soluble with low molecular weights (<3 kDa) and that action could be through the following five compounds: ergothioneine, adenine, guanine, hypoxanthine, and xanthine, which are present in all fractions (UF-3, AqF-3 kDa and organic fractions) showing NS3/4A inhibition. Low molecular weight aqueous extracts (<3 kDa) from A. bisporus have potential applications in the prophylaxis and treatment of HCV, especially for patients who do not have access to the last generation of DAAs. They may be useful as well for other flaviviruses, which also possess a NS3 serine protease.


Assuntos
Agaricus/química , Antivirais/isolamento & purificação , Antivirais/farmacologia , Hepacivirus/efeitos dos fármacos , Extratos Vegetais/isolamento & purificação , Extratos Vegetais/farmacologia , Replicação Viral/efeitos dos fármacos , Antivirais/química , Hepacivirus/enzimologia , Hepacivirus/genética , Hepacivirus/fisiologia , Hepatite C/virologia , Humanos , Extratos Vegetais/química , Inibidores de Proteases/química , Inibidores de Proteases/isolamento & purificação , Inibidores de Proteases/farmacologia , Espectrometria de Massas em Tandem , Proteínas não Estruturais Virais/antagonistas & inibidores , Proteínas não Estruturais Virais/genética , Proteínas não Estruturais Virais/metabolismo
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