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1.
Spectrochim Acta A Mol Biomol Spectrosc ; 244: 118825, 2021 Jan 05.
Artículo en Inglés | MEDLINE | ID: mdl-32866803

RESUMEN

Novel antiviral active molecule 2- [(4,6-diaminopyrimidin-2-yl)sulfanyl]-N-(4-fluoro- phenyl)acetamide has been synthesised and characterized by FT-IR and FT-Raman spectra. The equilibrium geometry, natural bond orbital calculations and vibrational assignments have been carried out using density functional B3LYP method with the 6-311G++(d,p) basis set. The complete vibrational assignments for all the vibrational modes have been supported by normal coordinate analysis, force constants and potential energy distributions. A detailed analysis of the intermolecular interactions has been performed based on the Hirshfeld surfaces. Drug likeness has been carried out based on Lipinski's rule and the absorption, distribution, metabolism, excretion and toxicity of the title molecule has been calculated. Antiviral potency of 2- [(4,6-diaminopyrimidin-2-yl)sulfanyl]-N-(4-fluoro-phenyl) acetamide has been investigated by docking against SARS-CoV-2 protein. The optimized geometry shows near-planarity between the phenyl ring and the pyrimidine ring. Differences in the geometries due to the substitution of the most electronegative fluorine atom and intermolecular contacts due to amino pyrimidine were analyzed. NBO analysis reveals the formation of two strong stable hydrogen bonded N-H···N intermolecular interactions and weak intramolecular interactions C-H···O and N-H···O. The Hirshfeld surfaces and consequently the 2D-fingerprint confirm the nature of intermolecular interactions and their quantitative contributions towards the crystal packing. The red shift in N-H stretching frequency exposed from IR substantiate the formation of N-H···N intermolecular hydrogen bond. Drug likeness and absorption, distribution, metabolism, excretion and toxicity properties analysis gives an idea about the pharmacokinetic properties of the title molecule. The binding energy -8.7 kcal/mol of the nonbonding interaction present a clear view that 2- [(4,6-diaminopyrimidin-2-yl)sulfanyl]-N-(4-fluoro- phenyl) acetamide can irreversibly interact with SARS-CoV-2 protease.


Asunto(s)
Acetamidas/química , Antivirales/química , Betacoronavirus/efectos de los fármacos , Infecciones por Coronavirus/tratamiento farmacológico , Pandemias , Neumonía Viral/tratamiento farmacológico , Inhibidores de Proteasas/química , Pirimidinas/química , Proteínas no Estructurales Virales/antagonistas & inhibidores , Acetamidas/farmacocinética , Antivirales/farmacocinética , Betacoronavirus/enzimología , Cristalografía por Rayos X , Cisteína Endopeptidasas , Humanos , Modelos Moleculares , Simulación del Acoplamiento Molecular , Estructura Molecular , Dinámicas no Lineales , Inhibidores de Proteasas/farmacocinética , Conformación Proteica , Pirimidinas/farmacocinética , Teoría Cuántica , Espectroscopía Infrarroja por Transformada de Fourier , Espectrometría Raman , Termodinámica , Vibración
2.
J Mol Model ; 26(12): 340, 2020 Nov 12.
Artículo en Inglés | MEDLINE | ID: mdl-33184722

RESUMEN

Among targets selected for studies aimed at identifying potential inhibitors against COVID-19, SARS-CoV2 main proteinase (Mpro) is highlighted. Mpro is indispensable for virus replication and is a promising target of potential inhibitors of COVID-19. Recently, monomeric SARS-CoV2 Mpro, drug repurposing, and docking methods have facilitated the identification of several potential inhibitors. Results were refined through the assessment of dimeric SARS-CoV2 Mpro, which represents the functional state of enzyme. Docking and molecular dynamics (MD) simulations combined with molecular mechanics/generalized Born surface area (MM/GBSA) studies indicated that dimeric Mpro most significantly impacts binding affinity tendency compared with the monomeric state, which suggests that dimeric state is most useful when performing studies aimed at identifying drugs targeting Mpro. In this study, we extend previous research by performing docking and MD simulation studies coupled with an MM/GBSA approach to assess binding of dimeric SARS-CoV2 Mpro to 12 FDA-approved drugs (darunavir, indinavir, saquinavir, tipranavir, diosmin, hesperidin, rutin, raltegravir, velpatasvir, ledipasvir, rosuvastatin, and bortezomib), which were identified as the best candidates for the treatment of COVID-19 in some previous dockings studies involving monomeric SARS-CoV2 Mpro. This analysis identified saquinavir as a potent inhibitor of dimeric SARS-CoV2 Mpro; therefore, the compound may have clinical utility against COVID-19. Graphical abstract.


Asunto(s)
Antivirales/farmacología , Betacoronavirus/efectos de los fármacos , Infecciones por Coronavirus/tratamiento farmacológico , Neumonía Viral/tratamiento farmacológico , Inhibidores de Proteasas/farmacología , Saquinavir/farmacología , Proteínas no Estructurales Virales/antagonistas & inhibidores , Antivirales/química , Betacoronavirus/enzimología , Infecciones por Coronavirus/virología , Cisteína Endopeptidasas , Reposicionamiento de Medicamentos , Humanos , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , Pandemias , Neumonía Viral/virología , Inhibidores de Proteasas/química , Multimerización de Proteína , Saquinavir/química
3.
J Mol Model ; 26(12): 341, 2020 Nov 16.
Artículo en Inglés | MEDLINE | ID: mdl-33200284

RESUMEN

HER-2 type breast cancer is one of the most aggressive malignancies found in women. Tucatinib is recently developed and approved as a potential medicine to fight this disease. In this manuscript, we present the gross structural features of this compound and its reactivity and wave function properties using computational simulations. Density functional theory was used to optimise the ground state geometry of the molecule and molecular docking was used to predict biological activity. As the electrons interact with electromagnetic radiations, electronic excitations between different energy levels are analysed in detail using time-dependent density functional theory. Various intermolecular and intermolecular interactions are analysed and reaction sites for attacking electrophiles and nucleophiles identified. Information entropy calculations show that the compound is inherently stable. Docking with COVID-19 proteins show docking score of - 9.42, - 8.93, - 8.45 and - 8.32 kcal/mol respectively indicating high interaction between the drug and proteins. Hence, this is an ideal candidate to study repurposing of existing drugs to combat the pandemic.


Asunto(s)
Antineoplásicos/química , Antivirales/química , Betacoronavirus/química , Electrones , Oxazoles/química , Inhibidores de Proteasas/química , Piridinas/química , Quinazolinas/química , Proteínas no Estructurales Virales/antagonistas & inhibidores , Antineoplásicos/metabolismo , Antivirales/metabolismo , Betacoronavirus/enzimología , Sitios de Unión , Cisteína Endopeptidasas/química , Cisteína Endopeptidasas/metabolismo , Reposicionamiento de Medicamentos , Humanos , Enlace de Hidrógeno , Interacciones Hidrofóbicas e Hidrofílicas , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , Oxazoles/metabolismo , Inhibidores de Proteasas/metabolismo , Unión Proteica , Dominios y Motivos de Interacción de Proteínas , Estructura Secundaria de Proteína , Piridinas/metabolismo , Teoría Cuántica , Quinazolinas/metabolismo , Termodinámica , Proteínas no Estructurales Virales/química , Proteínas no Estructurales Virales/metabolismo
4.
Sci Rep ; 10(1): 19522, 2020 11 11.
Artículo en Inglés | MEDLINE | ID: mdl-33177594

RESUMEN

SARS-CoV-2, the pathogenic agent of COVID-19, employs angiotensin converting enzyme-2 (ACE2) as its cell entry receptor. Clinical data reveal that in severe COVID-19, SARS-CoV-2 infects the lung, leading to a frequently lethal triad of respiratory insufficiency, acute cardiovascular failure, and coagulopathy. Physiologically, ACE2 plays a role in the regulation of three systems that could potentially be involved in the pathogenesis of severe COVID-19: the kinin-kallikrein system, resulting in acute lung inflammatory edema; the renin-angiotensin system, promoting cardiovascular instability; and the coagulation system, leading to thromboembolism. Here we assembled a healthy human lung cell atlas meta-analysis with ~ 130,000 public single-cell transcriptomes and show that key elements of the bradykinin, angiotensin and coagulation systems are co-expressed with ACE2 in alveolar cells and associated with their differentiation dynamics, which could explain how changes in ACE2 promoted by SARS-CoV-2 cell entry result in the development of the three most severe clinical components of COVID-19.


Asunto(s)
Betacoronavirus/genética , Coagulación Sanguínea , Perfilación de la Expresión Génica , Sistema Calicreína-Quinina/genética , Peptidil-Dipeptidasa A/genética , Alveolos Pulmonares/citología , Sistema Renina-Angiotensina/genética , Betacoronavirus/enzimología , Betacoronavirus/fisiología , Humanos , Alveolos Pulmonares/metabolismo , Serina Endopeptidasas/genética
5.
F1000Res ; 9: 1166, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-33204411

RESUMEN

Background: The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), took more lives than combined epidemics of SARS, MERS, H1N1, and Ebola. Currently, the prevention and control of spread are the goals in COVID-19 management as there are no specific drugs to cure or vaccines available for prevention. Hence, the drug repurposing was explored by many research groups, and many target proteins have been examined. The major protease (M pro), and RNA-dependent RNA polymerase (RdRp) are two target proteins in SARS-CoV-2 that have been validated and extensively studied for drug development in COVID-19. The RdRp shares a high degree of homology between those of two previously known coronaviruses, SARS-CoV and MERS-CoV. Methods: In this study, the FDA approved library of drugs were docked against the active site of RdRp using Schrodinger's computer-aided drug discovery tools for in silico drug-repurposing. Results: We have shortlisted 14 drugs from the Standard Precision docking and interaction-wise study of drug-binding with the active site on the enzyme. These drugs are antibiotics, NSAIDs, hypolipidemic, coagulant, thrombolytic, and anti-allergics. In molecular dynamics simulations, pitavastatin, ridogrel and rosoxacin displayed superior binding with the active site through ARG555 and divalent magnesium. Conclusion: Pitavastatin, ridogrel and rosoxacin can be further optimized in preclinical and clinical studies to determine their possible role in COVID-19 treatment.


Asunto(s)
Antivirales , Infecciones por Coronavirus/tratamiento farmacológico , Reposicionamiento de Medicamentos , Neumonía Viral/tratamiento farmacológico , /antagonistas & inhibidores , Antivirales/farmacología , Betacoronavirus/efectos de los fármacos , Betacoronavirus/enzimología , Dominio Catalítico , Humanos , Simulación del Acoplamiento Molecular , Pandemias , Ácidos Pentanoicos/farmacología , Piridinas/farmacología , Quinolinas/farmacología , Quinolonas/farmacología
6.
Nat Commun ; 11(1): 5877, 2020 11 18.
Artículo en Inglés | MEDLINE | ID: mdl-33208735

RESUMEN

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the pathogen that causes the disease COVID-19, produces replicase polyproteins 1a and 1ab that contain, respectively, 11 or 16 nonstructural proteins (nsp). Nsp5 is the main protease (Mpro) responsible for cleavage at eleven positions along these polyproteins, including at its own N- and C-terminal boundaries, representing essential processing events for subsequent viral assembly and maturation. We have determined X-ray crystallographic structures of this cysteine protease in its wild-type free active site state at 1.8 Å resolution, in its acyl-enzyme intermediate state with the native C-terminal autocleavage sequence at 1.95 Å resolution and in its product bound state at 2.0 Å resolution by employing an active site mutation (C145A). We characterize the stereochemical features of the acyl-enzyme intermediate including critical hydrogen bonding distances underlying catalysis in the Cys/His dyad and oxyanion hole. We also identify a highly ordered water molecule in a position compatible for a role as the deacylating nucleophile in the catalytic mechanism and characterize the binding groove conformational changes and dimerization interface that occur upon formation of the acyl-enzyme. Collectively, these crystallographic snapshots provide valuable mechanistic and structural insights for future antiviral therapeutic development including revised molecular docking strategies based on Mpro inhibition.


Asunto(s)
Betacoronavirus/enzimología , Cisteína Endopeptidasas/química , Proteínas no Estructurales Virales/química , Betacoronavirus/química , Sitios de Unión , Dominio Catalítico , Cristalografía por Rayos X , Cisteína Endopeptidasas/genética , Cisteína Endopeptidasas/metabolismo , Dimerización , Humanos , Modelos Moleculares , Mutación , Inhibidores de Proteasas/metabolismo , Conformación Proteica , Especificidad por Sustrato , Proteínas no Estructurales Virales/antagonistas & inhibidores , Proteínas no Estructurales Virales/genética , Proteínas no Estructurales Virales/metabolismo
7.
Phys Chem Chem Phys ; 22(43): 25335-25343, 2020 Nov 21.
Artículo en Inglés | MEDLINE | ID: mdl-33140777

RESUMEN

Coronavirus disease 2019 (COVID-19) is an ongoing global pandemic with very limited specific treatments. To fight COVID-19, various traditional antiviral medicines have been prescribed in China to infected patients with mild to moderate symptoms and received unexpected success in controlling the disease. However, the molecular mechanisms of how these herbal medicines interact with the SARS-CoV-2 virus that causes COVID-19 have remained elusive. It is well known that the main protease (Mpro) of SARS-CoV-2 plays an important role in maturation of many viral proteins such as the RNA-dependent RNA polymerase. Here, we explore the underlying molecular mechanisms of the computationally determined top candidate, namely, rutin which is a key component in many traditional antiviral medicines such as Lianhuaqinwen and Shuanghuanlian, for inhibiting the viral target-Mpro. Using in silico methods (docking and molecular dynamics simulations), we revealed the dynamics and energetics of rutin when interacting with the Mpro of SARS-CoV-2, suggesting that the highly hydrophilic rutin molecule can be bound inside the Mpro's pocket (active site) and possibly inhibit its biological functions. In addition, we optimized the structure of rutin and designed two more hydrophobic analogs, M1 and M2, which satisfy the rule of five for western medicines and demonstrated that they (M2 in particular) possess much stronger binding affinities to the SARS-COV-2s Mpro than rutin, due to the enhanced hydrophobic interaction as well as more hydrogen bonds. Therefore, our results provide invaluable insights into the mechanism of a ligand's binding inside the Mpro and shed light on future structure-based designs of high-potent inhibitors for SARS-CoV-2 Mpro.


Asunto(s)
Betacoronavirus/enzimología , Cisteína Endopeptidasas/metabolismo , Inhibidores de Proteasas/química , Rutina/química , Proteínas no Estructurales Virales/metabolismo , Betacoronavirus/aislamiento & purificación , Sitios de Unión , Infecciones por Coronavirus/patología , Infecciones por Coronavirus/virología , Cisteína Endopeptidasas/química , Medicina de Hierbas , Humanos , Enlace de Hidrógeno , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , Pandemias , Neumonía Viral/patología , Neumonía Viral/virología , Inhibidores de Proteasas/metabolismo , Dominios Proteicos , Rutina/metabolismo , Termodinámica , Proteínas no Estructurales Virales/química
8.
J Phys Chem Lett ; 11(21): 9144-9151, 2020 Nov 05.
Artículo en Inglés | MEDLINE | ID: mdl-33052685

RESUMEN

The raging COVID-19 pandemic caused by SARS-CoV-2 has infected tens of millions of people and killed several hundred thousand patients worldwide. Currently, there are no effective drugs or vaccines available for treating coronavirus infections. In this study, we have focused on the SARS-CoV-2 helicase (Nsp13), which is critical for viral replication and the most conserved nonstructural protein within the coronavirus family. Using homology modeling that couples published electron-density with molecular dynamics (MD)-based structural refinements, we generated structural models of the SARS-CoV-2 helicase in its apo- and ATP/RNA-bound conformations. We performed virtual screening of ∼970 000 chemical compounds against the ATP-binding site to identify potential inhibitors. Herein, we report docking hits of approved human drugs targeting the ATP-binding site. Importantly, two of our top drug hits have significant activity in inhibiting purified recombinant SARS-CoV-2 helicase, providing hope that these drugs can be potentially repurposed for the treatment of COVID-19.


Asunto(s)
Antivirales/química , Betacoronavirus/enzimología , ARN Helicasas/antagonistas & inhibidores , Proteínas no Estructurales Virales/antagonistas & inhibidores , Adenosina Trifosfato/química , Adenosina Trifosfato/metabolismo , Secuencia de Aminoácidos , Antivirales/metabolismo , Antivirales/uso terapéutico , Betacoronavirus/aislamiento & purificación , Sitios de Unión , Infecciones por Coronavirus/tratamiento farmacológico , Infecciones por Coronavirus/virología , Humanos , Interacciones Hidrofóbicas e Hidrofílicas , Simulación de Dinámica Molecular , Pandemias , Neumonía Viral/tratamiento farmacológico , Neumonía Viral/virología , Estructura Terciaria de Proteína , ARN Helicasas/química , ARN Helicasas/metabolismo , Proteínas no Estructurales Virales/química , Proteínas no Estructurales Virales/metabolismo
9.
SAR QSAR Environ Res ; 31(11): 857-867, 2020 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-33100032

RESUMEN

A novel coronavirus recently identified in Wuhan, China (2019-nCoV) has resulted in an increasing number of patients globally, and has become a highly lethal pathogenic member of the coronavirus family affecting humans. 2019-nCoV has established itself as one of the most threatening pandemics that human beings have faced, and therefore analysis and evaluation of all possible responses against infection is required. One such strategy includes utilizing the knowledge gained from the SARS and MERS outbreaks regarding existing antivirals. Indicating a potential for success, one of the drugs, remdesivir, under repurposing studies, has shown positive results in initial clinical studies. Therefore, in the current work, the authors have attempted to utilize the remdesivir-RdRp complex - RdRp (RNA-dependent RNA polymerase) being the putative target for remdesivir - to screen a library of the already reported RdRp inhibitor database. Further clustering on the basis of structural features and scoring refinement was performed to filter out false positive hits. Finally, molecular dynamics simulation was carried out to validate the identification of hits as RdRp inhibitors against novel coronavirus 2019-nCoV. The results yielded two putative hits which can inhibit RdRp with better potency than remdesivir, subject to further biological evaluation.


Asunto(s)
Adenosina Monofosfato/análogos & derivados , Alanina/análogos & derivados , Antivirales/farmacología , Simulación del Acoplamiento Molecular , /antagonistas & inhibidores , Adenosina Monofosfato/química , Adenosina Monofosfato/farmacología , Alanina/química , Alanina/farmacología , Antivirales/química , Betacoronavirus/efectos de los fármacos , Betacoronavirus/enzimología , Infecciones por Coronavirus/tratamiento farmacológico , Pandemias , Neumonía Viral , Relación Estructura-Actividad Cuantitativa , Proteínas Virales/efectos de los fármacos
10.
Pharmacol Res Perspect ; 8(6): e00674, 2020 12.
Artículo en Inglés | MEDLINE | ID: mdl-33124786

RESUMEN

SARS-CoV-2, a member of the coronavirus family, has caused a global public health emergency. Based on our analysis of hepatitis C virus and coronavirus replication, and the molecular structures and activities of viral inhibitors, we previously reasoned that the FDA-approved hepatitis C drug EPCLUSA (Sofosbuvir/Velpatasvir) should inhibit coronaviruses, including SARS-CoV-2. Here, using model polymerase extension experiments, we demonstrate that the active triphosphate form of Sofosbuvir is incorporated by low-fidelity polymerases and SARS-CoV RNA-dependent RNA polymerase (RdRp), and blocks further incorporation by these polymerases; the active triphosphate form of Sofosbuvir is not incorporated by a host-like high-fidelity DNA polymerase. Using the same molecular insight, we selected 3'-fluoro-3'-deoxythymidine triphosphate and 3'-azido-3'-deoxythymidine triphosphate, which are the active forms of two other anti-viral agents, Alovudine and AZT (an FDA-approved HIV/AIDS drug) for evaluation as inhibitors of SARS-CoV RdRp. We demonstrate the ability of two of these HIV reverse transcriptase inhibitors to be incorporated by SARS-CoV RdRp where they also terminate further polymerase extension. Given the 98% amino acid similarity of the SARS-CoV and SARS-CoV-2 RdRps, we expect these nucleotide analogues would also inhibit the SARS-CoV-2 polymerase. These results offer guidance to further modify these nucleotide analogues to generate more potent broad-spectrum anti-coronavirus agents.


Asunto(s)
Antivirales/farmacología , Betacoronavirus/efectos de los fármacos , Infecciones por Coronavirus/tratamiento farmacológico , Neumonía Viral/tratamiento farmacológico , /antagonistas & inhibidores , Betacoronavirus/enzimología , Carbamatos/farmacología , Infecciones por Coronavirus/virología , Didesoxinucleótidos/farmacología , Combinación de Medicamentos , Compuestos Heterocíclicos de 4 o más Anillos/farmacología , Humanos , Pandemias , Neumonía Viral/virología , Sofosbuvir/farmacología , Nucleótidos de Timina/farmacología , Zidovudina/análogos & derivados , Zidovudina/farmacología
11.
J Chem Theory Comput ; 16(11): 7160-7172, 2020 Nov 10.
Artículo en Inglés | MEDLINE | ID: mdl-33090785

RESUMEN

In the context of drug-receptor binding affinity calculations using molecular dynamics techniques, we implemented a combination of Hamiltonian replica exchange (HREM) and a novel nonequilibrium alchemical methodology, called virtual double-system single-box, with increased accuracy, precision, and efficiency with respect to the standard nonequilibrium approaches. The method has been applied for the determination of absolute binding free energies of 16 newly designed noncovalent ligands of the main protease (3CLpro) of SARS-CoV-2. The core structures of 3CLpro ligands were previously identified using a multimodal structure-based ligand design in combination with docking techniques. The calculated binding free energies for four additional ligands with known activity (either for SARS-CoV or SARS-CoV-2 main protease) are also reported. The nature of binding in the 3CLpro active site and the involved residues besides the CYS-HYS catalytic dyad have been thoroughly characterized by enhanced sampling simulations of the bound state. We have identified several noncongeneric compounds with predicted low micromolar activity for 3CLpro inhibition, which may constitute possible lead compounds for the development of antiviral agents in Covid-19 treatment.


Asunto(s)
Betacoronavirus/enzimología , Cisteína Endopeptidasas/metabolismo , Proteínas no Estructurales Virales/metabolismo , Antivirales/farmacología , Antivirales/uso terapéutico , Infecciones por Coronavirus/tratamiento farmacológico , Infecciones por Coronavirus/virología , Humanos , Ligandos , Simulación del Acoplamiento Molecular , Pandemias , Neumonía Viral/tratamiento farmacológico , Neumonía Viral/virología , Inhibidores de Proteasas/farmacología , Inhibidores de Proteasas/uso terapéutico , Unión Proteica , Interfaz Usuario-Computador , Proteínas no Estructurales Virales/antagonistas & inhibidores
12.
J Proteome Res ; 19(11): 4316-4326, 2020 11 06.
Artículo en Inglés | MEDLINE | ID: mdl-33090793

RESUMEN

The unprecedented pandemic of coronavirus disease 2019 (COVID-19) demands effective treatment for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. The infection of SARS-CoV-2 critically depends on diverse viral or host proteases, which mediate viral entry, viral protein maturation, as well as the pathogenesis of the viral infection. Endogenous and exogenous agents targeting for proteases have been proved to be effective toward a variety of viral infections ranging from HIV to influenza virus, suggesting protease inhibitors as a promising antiviral treatment for COVID-19. In this Review, we discuss how host and viral proteases participated in the pathogenesis of COVID-19 as well as the prospects and ongoing clinical trials of protease inhibitors as treatments.


Asunto(s)
Antivirales , Betacoronavirus , Infecciones por Coronavirus , Pandemias , Neumonía Viral , Inhibidores de Proteasas , Betacoronavirus/efectos de los fármacos , Betacoronavirus/enzimología , Infecciones por Coronavirus/tratamiento farmacológico , Infecciones por Coronavirus/fisiopatología , Infecciones por Coronavirus/virología , Interacciones Huésped-Patógeno , Humanos , Péptido Hidrolasas , Peptidil-Dipeptidasa A , Neumonía Viral/tratamiento farmacológico , Neumonía Viral/fisiopatología , Neumonía Viral/virología , Serina Endopeptidasas , Proteínas Virales
13.
Molecules ; 25(19)2020 Oct 06.
Artículo en Inglés | MEDLINE | ID: mdl-33036293

RESUMEN

A novel series of some hydrazones bearing thiazole moiety were generated via solvent-drop grinding of thiazole carbohydrazide 2 with various carbonyl compounds. Also, dehydrative-cyclocondensation of 2 with active methylene compounds or anhydrides gave the respective pyarzole or pyrazine derivatives. The structures of the newly synthesized compounds were established based on spectroscopic evidences and their alternative syntheses. Additionally, the anti-viral activity of all the products was tested against SARS-CoV-2 main protease (Mpro) using molecular docking combined with molecular dynamics simulation (MDS). The average binding affinities of the compounds 3a, 3b, and 3c (-8.1 ± 0.33 kcal/mol, -8.0 ± 0.35 kcal/mol, and -8.2 ± 0.21 kcal/mol, respectively) are better than that of the positive control Nelfinavir (-6.9 ± 0.51 kcal/mol). This shows the possibility of these three compounds to effectively bind to SARS-CoV-2 Mpro and hence, contradict the virus lifecycle.


Asunto(s)
Antivirales/síntesis química , Betacoronavirus/enzimología , Hidrazonas/síntesis química , Inhibidores de Proteasas/síntesis química , Pirazinas/síntesis química , Pirazoles/síntesis química , Proteínas no Estructurales Virales/antagonistas & inhibidores , Antivirales/farmacología , Betacoronavirus/química , Betacoronavirus/efectos de los fármacos , Sitios de Unión , Infecciones por Coronavirus/tratamiento farmacológico , Cisteína Endopeptidasas/química , Cisteína Endopeptidasas/metabolismo , Descubrimiento de Drogas , Humanos , Hidrazonas/farmacología , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , Pandemias , Neumonía Viral/tratamiento farmacológico , Inhibidores de Proteasas/farmacología , Unión Proteica , Conformación Proteica en Hélice alfa , Conformación Proteica en Lámina beta , Dominios y Motivos de Interacción de Proteínas , Pirazinas/farmacología , Pirazoles/farmacología , Termodinámica , Interfaz Usuario-Computador , Proteínas no Estructurales Virales/química , Proteínas no Estructurales Virales/metabolismo
14.
Acta Crystallogr F Struct Biol Commun ; 76(Pt 10): 483-487, 2020 Oct 01.
Artículo en Inglés | MEDLINE | ID: mdl-33006576

RESUMEN

The replication of SARS-CoV-2 produces two large polyproteins, pp1a and pp1ab, that are inactive until cleavage by the viral chymotrypsin-like cysteine protease enzyme (3CL Mpro) into a series of smaller functional proteins. At the heart of 3CL Mpro is an unusual catalytic dyad formed by the side chains of His41 and Cys145 and a coordinated water molecule. The catalytic mechanism by which the enzyme operates is still unknown, as crucial information on the protonation states within the active site is unclear. To experimentally determine the protonation states of the catalytic site and of the other residues in the substrate-binding cavity, and to visualize the hydrogen-bonding networks throughout the enzyme, room-temperature neutron and X-ray data were collected from a large H/D-exchanged crystal of ligand-free (apo) 3CL Mpro.


Asunto(s)
Betacoronavirus/enzimología , Infecciones por Coronavirus/virología , Cisteína Endopeptidasas/química , Neumonía Viral/virología , Proteínas no Estructurales Virales/química , Betacoronavirus/química , Betacoronavirus/genética , Dominio Catalítico , Cristalografía por Rayos X , Cisteína Endopeptidasas/genética , Humanos , Modelos Moleculares , Difracción de Neutrones , Pandemias , Conformación Proteica , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Temperatura , Proteínas no Estructurales Virales/genética
15.
J Comput Aided Mol Des ; 34(12): 1237-1259, 2020 12.
Artículo en Inglés | MEDLINE | ID: mdl-33034007

RESUMEN

Computational protein-ligand docking is well-known to be prone to inaccuracies in input receptor structures, and it is challenging to obtain good docking results with computationally predicted receptor structures (e.g. through homology modeling). Here we introduce a fragment-based docking method and test if it reduces requirements on the accuracy of an input receptor structures relative to non-fragment docking approaches. In this method, small rigid fragments are docked first using AutoDock Vina to generate a large number of favorably docked poses spanning the receptor binding pocket. Then a graph theory maximum clique algorithm is applied to find combined sets of docked poses of different fragment types onto which the complete ligand can be properly aligned. On the basis of these alignments, possible binding poses of complete ligand are determined. This docking method is first tested for bound docking on a series of Cytochrome P450 (CYP450) enzyme-substrate complexes, in which experimentally determined receptor structures are used. For all complexes tested, ligand poses of less than 1 Å root mean square deviations (RMSD) from the actual binding positions can be recovered. Then the method is tested for unbound docking with modeled receptor structures for a number of protein-ligand complexes from different families including the very recent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) protease. For all complexes, poses with RMSD less than 3 Å from actual binding positions can be recovered. Our results suggest that for docking with approximately modeled receptor structures, fragment-based methods can be more effective than common complete ligand docking approaches.


Asunto(s)
Betacoronavirus/enzimología , Infecciones por Coronavirus/tratamiento farmacológico , Cisteína Endopeptidasas/efectos de los fármacos , Simulación del Acoplamiento Molecular , Pandemias , Neumonía Viral/tratamiento farmacológico , Proteínas no Estructurales Virales/efectos de los fármacos , ATPasas Asociadas con Actividades Celulares Diversas/química , ATPasas Asociadas con Actividades Celulares Diversas/metabolismo , Cisteína Endopeptidasas/química , Cisteína Endopeptidasas/metabolismo , Sistema Enzimático del Citocromo P-450/química , Sistema Enzimático del Citocromo P-450/metabolismo , Proteínas de Unión al ADN/química , Proteínas de Unión al ADN/metabolismo , Humanos , Ligandos , Modelos Químicos , Modelos Moleculares , Chaperonas Moleculares/química , Chaperonas Moleculares/metabolismo , Fragmentos de Péptidos/química , Fragmentos de Péptidos/metabolismo , Unión Proteica , Conformación Proteica , Receptores Acoplados a Proteínas G/química , Receptores Acoplados a Proteínas G/metabolismo , Factores de Transcripción/química , Factores de Transcripción/metabolismo , Proteínas no Estructurales Virales/química , Proteínas no Estructurales Virales/metabolismo
16.
Comput Biol Med ; 126: 104046, 2020 11.
Artículo en Inglés | MEDLINE | ID: mdl-33065388

RESUMEN

Coronavirus Disease 2019 (COVID-19) is an infectious illness caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), originally identified in Wuhan, China (December 2019) and has since expanded into a pandemic. Here, we investigate metabolites present in several common spices as possible inhibitors of COVID-19. Specifically, 32 compounds isolated from 14 cooking seasonings were examined as inhibitors for SARS-CoV-2 main protease (Mpro), which is required for viral multiplication. Using a drug discovery approach to identify possible antiviral leads, in silico molecular docking studies were performed. Docking calculations revealed a high potency of salvianolic acid A and curcumin as Mpro inhibitors with binding energies of -9.7 and -9.2 kcal/mol, respectively. Binding mode analysis demonstrated the ability of salvianolic acid A and curcumin to form nine and six hydrogen bonds, respectively with amino acids proximal to Mpro's active site. Stabilities and binding affinities of the two identified natural spices were calculated over 40 ns molecular dynamics simulations and compared to an antiviral protease inhibitor (lopinavir). Molecular mechanics-generalized Born surface area energy calculations revealed greater salvianolic acid A affinity for the enzyme over curcumin and lopinavir with energies of -44.8, -34.2 and -34.8 kcal/mol, respectively. Using a STRING database, protein-protein interactions were identified for salvianolic acid A included the biochemical signaling genes ACE, MAPK14 and ESR1; and for curcumin, EGFR and TNF. This study establishes salvianolic acid A as an in silico natural product inhibitor against the SARS-CoV-2 main protease and provides a promising inhibitor lead for in vitro enzyme testing.


Asunto(s)
Betacoronavirus/enzimología , Ácidos Cafeicos/química , Infecciones por Coronavirus/tratamiento farmacológico , Curcumina/química , Cisteína Endopeptidasas , Descubrimiento de Drogas , Lactatos/química , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , Neumonía Viral/tratamiento farmacológico , Inhibidores de Proteasas/química , Proteínas no Estructurales Virales , Ácidos Cafeicos/uso terapéutico , Infecciones por Coronavirus/enzimología , Curcumina/uso terapéutico , Cisteína Endopeptidasas/química , Humanos , Lactatos/uso terapéutico , Pandemias , Neumonía Viral/enzimología , Inhibidores de Proteasas/uso terapéutico , Termodinámica , Proteínas no Estructurales Virales/antagonistas & inhibidores , Proteínas no Estructurales Virales/química
17.
Molecules ; 25(20)2020 Oct 13.
Artículo en Inglés | MEDLINE | ID: mdl-33066278

RESUMEN

The global SARS-CoV-2 pandemic started late 2019 and currently continues unabated. The lag-time for developing vaccines means it is of paramount importance to be able to quickly develop and repurpose therapeutic drugs. Protein-based biosensors allow screening to be performed using routine molecular laboratory equipment without a need for expensive chemical reagents. Here we present a biosensor for the 3-chymotrypsin-like cysteine protease from SARS-CoV-2, comprising a FRET-capable pair of fluorescent proteins held in proximity by a protease cleavable linker. We demonstrate the utility of this biosensor for inhibitor discovery by screening 1280 compounds from the Library of Pharmaceutically Active Compounds collection. The screening identified 65 inhibitors, with the 20 most active exhibiting sub-micromolar inhibition of 3CLpro in follow-up EC50 assays. The top hits included several compounds not previously identified as 3CLpro inhibitors, in particular five members of a family of aporphine alkaloids that offer promise as new antiviral drug leads.


Asunto(s)
Betacoronavirus/efectos de los fármacos , Técnicas Biosensibles/métodos , Infecciones por Coronavirus/tratamiento farmacológico , Transferencia Resonante de Energía de Fluorescencia/métodos , Neumonía Viral/tratamiento farmacológico , Inhibidores de Proteasas/química , Inhibidores de Proteasas/farmacología , Proteínas no Estructurales Virales/antagonistas & inhibidores , Betacoronavirus/enzimología , Betacoronavirus/aislamiento & purificación , Infecciones por Coronavirus/virología , Cisteína Endopeptidasas , Ensayos Analíticos de Alto Rendimiento , Humanos , Pandemias , Neumonía Viral/virología
18.
Sci Adv ; 6(42)2020 10.
Artículo en Inglés | MEDLINE | ID: mdl-33067239

RESUMEN

Viral papain-like cysteine protease (PLpro, NSP3) is essential for SARS-CoV-2 replication and represents a promising target for the development of antiviral drugs. Here, we used a combinatorial substrate library and performed comprehensive activity profiling of SARS-CoV-2 PLpro. On the scaffold of the best hits from positional scanning, we designed optimal fluorogenic substrates and irreversible inhibitors with a high degree of selectivity for SARS PLpro. We determined crystal structures of two of these inhibitors in complex with SARS-CoV-2 PLpro that reveals their inhibitory mechanisms and provides a molecular basis for the observed substrate specificity profiles. Last, we demonstrate that SARS-CoV-2 PLpro harbors deISGylating activity similar to SARSCoV-1 PLpro but its ability to hydrolyze K48-linked Ub chains is diminished, which our sequence and structure analysis provides a basis for. Together, this work has revealed the molecular rules governing PLpro substrate specificity and provides a framework for development of inhibitors with potential therapeutic value or drug repurposing.


Asunto(s)
Betacoronavirus/enzimología , Diseño de Fármacos , Inhibidores de Proteasas/química , Proteínas no Estructurales Virales/antagonistas & inhibidores , Secuencia de Aminoácidos , Betacoronavirus/aislamiento & purificación , Sitios de Unión , Dominio Catalítico , Infecciones por Coronavirus/patología , Infecciones por Coronavirus/virología , Cristalografía por Rayos X , Cisteína Endopeptidasas/genética , Cisteína Endopeptidasas/metabolismo , Humanos , Cinética , Simulación de Dinámica Molecular , Oligopéptidos/química , Oligopéptidos/metabolismo , Pandemias , Neumonía Viral/patología , Neumonía Viral/virología , Inhibidores de Proteasas/metabolismo , Proteínas Recombinantes/biosíntesis , Proteínas Recombinantes/química , Proteínas Recombinantes/aislamiento & purificación , Especificidad por Sustrato , Ubiquitinas/metabolismo , Proteínas no Estructurales Virales/genética , Proteínas no Estructurales Virales/metabolismo
19.
Sci Rep ; 10(1): 16577, 2020 10 06.
Artículo en Inglés | MEDLINE | ID: mdl-33024223

RESUMEN

SARS-CoV-2 is responsible for COVID-19, resulting in the largest pandemic in over a hundred years. After examining the molecular structures and activities of hepatitis C viral inhibitors and comparing hepatitis C virus and coronavirus replication, we previously postulated that the FDA-approved hepatitis C drug EPCLUSA (Sofosbuvir/Velpatasvir) might inhibit SARS-CoV-2. We subsequently demonstrated that Sofosbuvir triphosphate is incorporated by the relatively low fidelity SARS-CoV and SARS-CoV-2 RNA-dependent RNA polymerases (RdRps), serving as an immediate polymerase reaction terminator, but not by a host-like high fidelity DNA polymerase. Other investigators have since demonstrated the ability of Sofosbuvir to inhibit SARS-CoV-2 replication in lung and brain cells; additionally, COVID-19 clinical trials with EPCLUSA and with Sofosbuvir plus Daclatasvir have been initiated in several countries. SARS-CoV-2 has an exonuclease-based proofreader to maintain the viral genome integrity. Any effective antiviral targeting the SARS-CoV-2 RdRp must display a certain level of resistance to this proofreading activity. We report here that Sofosbuvir terminated RNA resists removal by the exonuclease to a substantially higher extent than RNA terminated by Remdesivir, another drug being used as a COVID-19 therapeutic. These results offer a molecular basis supporting the current use of Sofosbuvir in combination with other drugs in COVID-19 clinical trials.


Asunto(s)
Adenosina Monofosfato/análogos & derivados , Alanina/análogos & derivados , Antivirales/farmacología , Betacoronavirus/efectos de los fármacos , Infecciones por Coronavirus/tratamiento farmacológico , Exonucleasas/metabolismo , Neumonía Viral/tratamiento farmacológico , Profármacos/farmacología , ARN Viral/efectos de los fármacos , Sofosbuvir/farmacología , Adenosina Monofosfato/química , Adenosina Monofosfato/farmacología , Adenosina Monofosfato/uso terapéutico , Alanina/química , Alanina/farmacología , Alanina/uso terapéutico , Antivirales/química , Antivirales/uso terapéutico , Betacoronavirus/enzimología , Infecciones por Coronavirus/virología , Descubrimiento de Drogas/métodos , Reposicionamiento de Medicamentos/métodos , Hepacivirus/efectos de los fármacos , Hepacivirus/enzimología , Hepatitis C/tratamiento farmacológico , Hepatitis C/virología , Humanos , Pandemias , Neumonía Viral/virología , Profármacos/uso terapéutico , ARN Viral/química , ARN Viral/metabolismo , /metabolismo , Sofosbuvir/química , Sofosbuvir/uso terapéutico , Proteínas no Estructurales Virales/antagonistas & inhibidores , Proteínas no Estructurales Virales/metabolismo , Replicación Viral/efectos de los fármacos
20.
Phys Chem Chem Phys ; 22(40): 23099-23106, 2020 Oct 21.
Artículo en Inglés | MEDLINE | ID: mdl-33025993

RESUMEN

COVID-19 has caused lockdowns all over the world in early 2020, as a global pandemic. Both theoretical and experimental efforts are seeking to find an effective treatment to suppress the virus. In silico drug design can play a vital role in identifying promising drug candidates against COVID-19. Herein, we focused on the main protease of SARS-CoV-2 that has crucial biological functions in the virus. We performed a ligand-based virtual screening followed by a docking screening for testing approved drugs and bioactive compounds listed in the DrugBank and ChEMBL databases. The top 8 docking results were advanced to all-atom MD simulations to study the relative stability of the protein-ligand interactions. MD simulations support that the catalytic residue, His41, has a neutral side chain with a protonated delta position. An absolute binding energy (ΔG) of -42 kJ mol-1 for the protein-ligand (Mpro-N3) complex has been calculated using the potential-of-mean-force (geometrical) approach. Furthermore, the relative binding energies were computed for the top docking results. Our results suggest several promising approved and bioactive inhibitors of SARS-CoV-2 Mpro as follows: a bioactive compound, ChEMBL275592, which has the best MM/GBSA binding energy; the second-best compound, montelukast, is an approved drug used in the treatment of asthma and allergic rhinitis; the third-best compound, ChEMBL288347, is a bioactive compound. Bromocriptine and saquinavir are other approved drugs that also demonstrate stability in the active site of Mpro, albeit their relative binding energies are low compared to the N3 inhibitor. This study provides useful insights into de novo protein design and novel inhibitor development, which could reduce the cost and time required for the discovery of a potent drug to combat SARS-CoV-2.


Asunto(s)
Betacoronavirus/enzimología , Inhibidores de Proteasas/química , Proteínas no Estructurales Virales/antagonistas & inhibidores , Antivirales/química , Antivirales/metabolismo , Betacoronavirus/aislamiento & purificación , Infecciones por Coronavirus/patología , Infecciones por Coronavirus/virología , Cisteína Endopeptidasas/metabolismo , Diseño de Fármacos , Humanos , Enlace de Hidrógeno , Ligandos , Pandemias , Neumonía Viral/patología , Neumonía Viral/virología , Inhibidores de Proteasas/metabolismo , Electricidad Estática , Termodinámica , Proteínas no Estructurales Virales/metabolismo
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