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1.
Int J Mol Sci ; 23(1)2022 Jan 04.
Article in English | MEDLINE | ID: covidwho-1613825

ABSTRACT

(1R,5S)-1-Hydroxy-3,6-dioxa-bicyclo[3.2.1]octan-2-one, available by an efficient catalytic pyrolysis of cellulose, has been applied as a chiral building block in the synthesis of seven new nucleoside analogues, with structural modifications on the nucleobase moiety and on the carboxyl- derived unit. The inverted configuration by Mitsunobu reaction used in their synthesis was verified by 2D-NOESY correlations, supported by the optimized structure employing the DFT methods. An in silico screening of these compounds as inhibitors of SARS-CoV-2 RNA-dependent RNA polymerase has been carried out in comparison with both remdesivir, a mono-phosphoramidate prodrug recently approved for COVID-19 treatment, and its ribonucleoside metabolite GS-441524. Drug-likeness prediction and data by docking calculation indicated compound 6 [=(3S,5S)-methyl 5-(hydroxymethyl)-3-(6-(4-methylpiperazin-1-yl)-9H-purin-9-yl)tetrahydrofuran-3-carboxylate] as the best candidate. Furthermore, molecular dynamics simulation showed a stable interaction of structure 6 in RNA-dependent RNA polymerase (RdRp) complex and a lower average atomic fluctuation than GS-441524, suggesting a well accommodation in the RdRp binding pocket.


Subject(s)
Antiviral Agents/chemical synthesis , Cellulose/chemistry , Coronavirus RNA-Dependent RNA Polymerase/antagonists & inhibitors , Nucleosides/chemical synthesis , SARS-CoV-2/enzymology , Adenosine/analogs & derivatives , Adenosine/chemistry , Adenosine/pharmacokinetics , Adenosine Monophosphate/analogs & derivatives , Adenosine Monophosphate/chemistry , Adenosine Monophosphate/pharmacokinetics , Alanine/analogs & derivatives , Alanine/chemistry , Alanine/pharmacokinetics , Antiviral Agents/chemistry , Antiviral Agents/pharmacokinetics , Computational Biology , Coronavirus RNA-Dependent RNA Polymerase/chemistry , Molecular Docking Simulation , Molecular Dynamics Simulation , Nucleosides/chemistry , Nucleosides/pharmacokinetics , Pyrolysis , SARS-CoV-2/drug effects
2.
Angew Chem Int Ed Engl ; 61(11): e202114619, 2022 03 07.
Article in English | MEDLINE | ID: covidwho-1544209

ABSTRACT

Since early 2020, scientists have strived to find an effective solution to fight SARS-CoV-2, in particular by developing reliable vaccines that inhibit the spread of the disease and repurposing drugs for combatting its effects on the human body. The antiviral prodrug Remdesivir is still the most widely used therapeutic during the early stages of the infection. However, the current synthetic routes rely on the use of protecting groups, air-sensitive reagents, and cryogenic conditions, thus impeding a cost-efficient supply to patients. We have, therefore, focused on the development of a straightforward, direct addition of (hetero)arenes to unprotected sugars. Here we report a silylium-catalyzed and completely stereoselective C-glycosylation that initially yields the open-chain polyols, which can be selectively cyclized to provide either the kinetic α-furanose or the thermodynamically favored ß-anomer. The method significantly expedites the synthesis of Remdesivir precursor GS-441524 after a subsequent Mn-catalyzed C-H oxidation and deoxycyanation.


Subject(s)
Adenosine Monophosphate/analogs & derivatives , Adenosine/analogs & derivatives , Alanine/analogs & derivatives , Antiviral Agents/chemical synthesis , Nucleosides/chemical synthesis , Adenosine/chemical synthesis , Adenosine/chemistry , Adenosine Monophosphate/chemical synthesis , Adenosine Monophosphate/chemistry , Alanine/chemical synthesis , Alanine/chemistry , Antiviral Agents/chemistry , COVID-19/drug therapy , Catalysis , Chemistry Techniques, Synthetic/economics , Chemistry Techniques, Synthetic/methods , Cyclization , Glycosylation , Humans , Models, Molecular , Nucleosides/chemistry , Stereoisomerism , Time Factors
3.
J Biol Chem ; 297(2): 100973, 2021 08.
Article in English | MEDLINE | ID: covidwho-1312455

ABSTRACT

N6-methyladenosine (m6A) is the most frequent chemical modification in eukaryotic mRNA and is known to participate in a variety of physiological processes, including cancer progression and viral infection. The reversible and dynamic m6A modification is installed by m6A methyltransferase (writer) enzymes and erased by m6A demethylase (eraser) enzymes. m6A modification recognized by m6A binding proteins (readers) regulates RNA processing and metabolism, leading to downstream biological effects such as promotion of stability and translation or increased degradation. The m6A writers and erasers determine the abundance of m6A modifications and play decisive roles in its distribution and function. In this review, we focused on m6A writers and erasers and present an overview on their known functions and enzymatic molecular mechanisms, showing how they recognize substrates and install or remove m6A modifications. We also summarize the current applications of m6A writers and erasers for m6A detection and highlight the merits and drawbacks of these available methods. Lastly, we describe the biological functions of m6A in cancers and viral infection based on research of m6A writers and erasers and introduce new assays for m6A functionality via programmable m6A editing tools.


Subject(s)
Adenosine/analogs & derivatives , Eukaryotic Cells/metabolism , Methyltransferases/metabolism , Neoplasms/pathology , RNA Processing, Post-Transcriptional/genetics , RNA, Messenger/genetics , Adenosine/chemistry , Adenosine/genetics , Adenosine/metabolism , Humans , Neoplasms/genetics , Neoplasms/metabolism
4.
mBio ; 12(4): e0106721, 2021 08 31.
Article in English | MEDLINE | ID: covidwho-1297962

ABSTRACT

The coronavirus disease 2019 pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is an ongoing global public crisis. Although viral RNA modification has been reported based on the transcriptome architecture, the types and functions of RNA modification are still unknown. In this study, we evaluated the roles of RNA N6-methyladenosine (m6A) modification in SARS-CoV-2. Our methylated RNA immunoprecipitation sequencing (MeRIP-Seq) and Nanopore direct RNA sequencing (DRS) analysis showed that SARS-CoV-2 RNA contained m6A modification. Moreover, SARS-CoV-2 infection not only increased the expression of methyltransferase-like 3 (METTL3) but also altered its distribution. Modification of METTL3 expression by short hairpin RNA or plasmid transfection for knockdown or overexpression, respectively, affected viral replication. Furthermore, the viral key protein RdRp interacted with METTL3, and METTL3 was distributed in both the nucleus and cytoplasm in the presence of RdRp. RdRp appeared to modulate the sumoylation and ubiquitination of METTL3 via an unknown mechanism. Taken together, our findings demonstrated that the host m6A modification complex interacted with viral proteins to modulate SARS-CoV-2 replication. IMPORTANCE Internal chemical modifications of viral RNA play key roles in the regulation of viral replication and gene expression. Although potential internal modifications have been reported in SARS-CoV-2 RNA, the function of the SARS-CoV-2 N6-methyladenosine (m6A) modification in the viral life cycle is unclear. In the current study, we demonstrated that SARS-CoV-2 RNA underwent m6A modification by host m6A machinery. SARS-CoV-2 infection altered the expression pattern of methyltransferases and demethylases, while the expression level of methyltransferase-like 3 (METTL3) and fat mass and obesity-associated protein (FTO) was linked to the viral replication. Further study showed that METTL3 interacted with viral RNA polymerase RNA-dependent RNA polymerase (RdRp), which influenced not only the distribution but also the posttranslational modification of METTL3. Our study provided evidence that host m6A components interacted with viral proteins to modulate viral replication.


Subject(s)
Adenosine/analogs & derivatives , Methyltransferases/genetics , Methyltransferases/metabolism , SARS-CoV-2/growth & development , Virus Replication/genetics , Adenosine/chemistry , Adenosine/genetics , Alpha-Ketoglutarate-Dependent Dioxygenase FTO/metabolism , COVID-19/pathology , Gene Expression Regulation/genetics , Humans , Methylation , Protein Processing, Post-Translational/physiology , RNA, Viral/chemistry , RNA, Viral/genetics , RNA-Dependent RNA Polymerase/genetics , SARS-CoV-2/genetics
5.
SLAS Discov ; 26(6): 757-765, 2021 07.
Article in English | MEDLINE | ID: covidwho-1194439

ABSTRACT

Frequent outbreaks of novel coronaviruses (CoVs), highlighted by the current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, necessitate the development of therapeutics that could be easily and effectively administered worldwide. The conserved mRNA-capping process enables CoVs to evade their host immune system and is a target for antiviral development. Nonstructural protein (nsp) 16 in complex with nsp10 catalyzes the final step of coronaviral mRNA capping through its 2'-O-methylation activity. Like other methyltransferases, the SARS-CoV-2 nsp10-nsp16 complex is druggable. However, the availability of an optimized assay for high-throughput screening (HTS) is an unmet need. Here, we report the development of a radioactivity-based assay for the methyltransferase activity of the nsp10-nsp16 complex in a 384-well format, kinetic characterization, and optimization of the assay for HTS (Z' factor = 0.83). Considering the high conservation of nsp16 across known CoV species, the potential inhibitors targeting the SARS-CoV-2 nsp10-nsp16 complex may also be effective against other emerging pathogenic CoVs.


Subject(s)
Adenosine/analogs & derivatives , High-Throughput Screening Assays , RNA Caps/antagonists & inhibitors , RNA, Viral/antagonists & inhibitors , Viral Nonstructural Proteins/antagonists & inhibitors , Viral Regulatory and Accessory Proteins/antagonists & inhibitors , Adenosine/chemistry , Adenosine/pharmacology , COVID-19/virology , Cloning, Molecular , Enzyme Assays , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/pharmacology , Escherichia coli/genetics , Escherichia coli/metabolism , Gene Expression , Genetic Vectors/chemistry , Genetic Vectors/metabolism , Humans , Kinetics , Methylation , Methyltransferases , Models, Molecular , RNA Caps/genetics , RNA Caps/metabolism , RNA, Viral/genetics , RNA, Viral/metabolism , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , SARS-CoV-2/drug effects , SARS-CoV-2/enzymology , SARS-CoV-2/genetics , Tritium , Viral Nonstructural Proteins/chemistry , Viral Nonstructural Proteins/genetics , Viral Nonstructural Proteins/metabolism , Viral Regulatory and Accessory Proteins/chemistry , Viral Regulatory and Accessory Proteins/genetics , Viral Regulatory and Accessory Proteins/metabolism
6.
J Enzyme Inhib Med Chem ; 36(1): 727-736, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1123193

ABSTRACT

The novel coronavirus disease COVID-19, caused by the virus SARS CoV-2, has exerted a significant unprecedented economic and medical crisis, in addition to its impact on the daily life and health care systems all over the world. Regrettably, no vaccines or drugs are currently available for this new critical emerging human disease. Joining the global fight against COVID-19, in this study we aim at identifying a potential novel inhibitor for SARS COV-2 2'-O-methyltransferase (nsp16) which is one of the most attractive targets in the virus life cycle, responsible for the viral RNA protection via a cap formation process. Firstly, nsp16 enzyme bound to Sinefungin was retrieved from the protein data bank (PDB ID: 6WKQ), then, a 3D pharmacophore model was constructed to be applied to screen 48 Million drug-like compounds of the Zinc database. This resulted in only 24 compounds which were subsequently docked into the enzyme. The best four score-ordered hits from the docking outcome exhibited better scores compared to Sinefungin. Finally, three molecular dynamics (MD) simulation experiments for 150 ns were carried out as a refinement step for our proposed approach. The MD and MM-PBSA outputs revealed compound 11 as the best potential nsp16 inhibitor herein identified, as it displayed a better stability and average binding free energy for the ligand-enzyme complex compared to Sinefungin.


Subject(s)
Antiviral Agents/chemistry , Enzyme Inhibitors/chemistry , SARS-CoV-2/enzymology , Viral Nonstructural Proteins/chemistry , Adenosine/analogs & derivatives , Adenosine/chemistry , Adenosine/metabolism , Antiviral Agents/metabolism , Binding Sites , Crystallography, X-Ray , Databases, Pharmaceutical , Databases, Protein , Drug Stability , Enzyme Inhibitors/metabolism , High-Throughput Screening Assays , Humans , Kinetics , Methyltransferases , Molecular Docking Simulation , Molecular Dynamics Simulation , Protein Binding , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Protein Interaction Domains and Motifs , SARS-CoV-2/chemistry , Thermodynamics , Viral Nonstructural Proteins/antagonists & inhibitors
7.
Med Hypotheses ; 149: 110543, 2021 Apr.
Article in English | MEDLINE | ID: covidwho-1087147

ABSTRACT

The socio-economic implications of COVID-19 are devastating. Considerable morbidity is attributed to 'long-COVID' - an increasingly recognized complication of infection. Its diverse symptoms are reminiscent of vitamin B12 deficiency, a condition in which methylation status is compromised. We suggest why SARS-CoV-2 infection likely leads to increased methyl-group requirements and other disturbances of one-carbon metabolism. We propose these might explain the varied symptoms of long-COVID. Our suggested mechanismmight also apply to similar conditions such as myalgic encephalomyelitis/chronic fatigue syndrome. The hypothesis is evaluable by detailed determination of vitamin B12and folate status, including serum formate as well as homocysteine and methylmalonic acid, and correlation with viral and host RNA methylation and symptomatology. If confirmed, methyl-group support should prove beneficial in such individuals.


Subject(s)
COVID-19/complications , Folic Acid/blood , Vitamin B 12 Deficiency/diagnosis , Adenosine/analogs & derivatives , Adenosine/chemistry , COVID-19/blood , COVID-19/physiopathology , Folic Acid Deficiency , Formates/blood , Genome, Viral , Glutathione/blood , Homocysteine/blood , Hospitalization , Humans , Methylation , Methylmalonic Acid/blood , Oxidative Stress , RNA/chemistry , Serine/blood , Vitamin B 12/blood
8.
J Med Chem ; 65(4): 2785-2793, 2022 02 24.
Article in English | MEDLINE | ID: covidwho-1057678

ABSTRACT

The outbreak of coronavirus disease 2019 (COVID-19) has resulted in a global pandemic due to the rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). At the time of this manuscript's publication, remdesivir is the only COVID-19 treatment approved by the United States Food and Drug Administration. However, its effectiveness is still under question due to the results of the large Solidarity Trial conducted by the World Health Organization. Herein, we report that the parent nucleoside of remdesivir, GS-441524, potently inhibits the replication of SARS-CoV-2 in Vero E6 and other cell lines. Challenge studies in both an AAV-hACE2 mouse model of SARS-CoV-2 and in mice infected with murine hepatitis virus, a closely related coronavirus, showed that GS-441524 was highly efficacious in reducing the viral titers in CoV-infected organs without notable toxicity. Our results support that GS-441524 is a promising and inexpensive drug candidate for treating of COVID-19 and other CoV diseases.


Subject(s)
Adenosine/analogs & derivatives , Antiviral Agents/pharmacology , COVID-19/drug therapy , Disease Models, Animal , Adenosine/chemistry , Adenosine/metabolism , Adenosine/pharmacology , Animals , Antiviral Agents/chemistry , Antiviral Agents/metabolism , COVID-19/metabolism , COVID-19/pathology , Cells, Cultured , Chlorocebus aethiops , Dose-Response Relationship, Drug , Humans , Male , Mice , Mice, Inbred BALB C , Microbial Sensitivity Tests , Molecular Structure , Structure-Activity Relationship
9.
Eur J Med Chem ; 187: 111956, 2020 Feb 01.
Article in English | MEDLINE | ID: covidwho-733871

ABSTRACT

We have reported on aristeromycin (1) and 6'-fluorinated-aristeromycin analogues (2), which are active against RNA viruses such as Middle East respiratory syndrome coronavirus (MERS-CoV), severe acute respiratory syndrome coronavirus (SARS-CoV), Zika virus (ZIKV), and Chikungunya virus (CHIKV). However, these exhibit substantial cytotoxicity. As this cytotoxicity may be attributed to 5'-phosphorylation, we designed and synthesized one-carbon homologated 6'-fluorinated-aristeromycin analogues. This modification prevents 5'-phosphorlyation by cellular kinases, whereas the inhibitory activity towards S-adenosyl-l-homocysteine (SAH) hydrolase will be retained. The enantiomerically pure 6'-fluorinated-5'-homoaristeromycin analogues 3a-e were synthesized via the electrophilic fluorination of the silyl enol ether with Selectfluor, using a base-build up approach as the key steps. All synthesized compounds exhibited potent inhibitory activity towards SAH hydrolase, among which 6'-ß-fluoroadenosine analogue 3a was the most potent (IC50 = 0.36 µM). Among the compounds tested, 6'-ß-fluoro-homoaristeromycin 3a showed potent antiviral activity (EC50 = 0.12 µM) against the CHIKV, without noticeable cytotoxicity up to 250 µM. Only 3a displayed anti-CHIKV activity, whereas both3a and 3b inhibited SAH hydrolase with similar IC50 values (0.36 and 0.37 µM, respectively), which suggested that 3a's antiviral activity did not merely depend on the inhibition of SAH hydrolase. This is further supported by the fact that the antiviral effect was specific for CHIKV and some other alphaviruses and none of the homologated analogues inhibited other RNA viruses, such as SARS-CoV, MERS-CoV, and ZIKV. The potent inhibition and high selectivity index make 6'-ß-fluoro-homoaristeromycin (3a) a promising new template for the development of antivirals against CHIKV, a serious re-emerging pathogen that has infected millions of people over the past 15 years.


Subject(s)
Adenosine/analogs & derivatives , Antiviral Agents/pharmacology , Chikungunya virus/drug effects , Adenosine/chemical synthesis , Adenosine/chemistry , Adenosine/pharmacology , Antiviral Agents/chemical synthesis , Antiviral Agents/chemistry , Crystallography, X-Ray , Dose-Response Relationship, Drug , Microbial Sensitivity Tests , Models, Molecular , Molecular Structure , Structure-Activity Relationship , Virus Replication/drug effects
10.
Sci Adv ; 6(23): eaaz5466, 2020 06.
Article in English | MEDLINE | ID: covidwho-602279

ABSTRACT

Uncontrolled inflammatory processes are at the root of numerous pathologies. Most recently, studies on confirmed COVID-19 cases have suggested that mortality might be due to virally induced hyperinflammation. Uncontrolled pro-inflammatory states are often driven by continuous positive feedback loops between pro-inflammatory signaling and oxidative stress, which cannot be resolved in a targeted manner. Here, we report on the development of multidrug nanoparticles for the mitigation of uncontrolled inflammation. The nanoparticles are made by conjugating squalene, a natural lipid, to adenosine, an endogenous immunomodulator, and then encapsulating α-tocopherol, as antioxidant. This resulted in high drug loading, biocompatible, multidrug nanoparticles. By exploiting the endothelial dysfunction at sites of acute inflammation, these multidrug nanoparticles delivered the therapeutic agents in a targeted manner, conferring survival advantage to treated animals in models of endotoxemia. Selectively delivering adenosine and antioxidants together could serve as a novel therapeutic approach for safe treatment of acute paradoxal inflammation.


Subject(s)
Drug Delivery Systems/methods , Endotoxemia/drug therapy , Nanoparticles/chemistry , Squalene/chemistry , Systemic Inflammatory Response Syndrome/drug therapy , Adenosine/administration & dosage , Adenosine/chemistry , Animals , Antioxidants/administration & dosage , Antioxidants/chemistry , Betacoronavirus , COVID-19 , Coronavirus Infections/drug therapy , Coronavirus Infections/pathology , Coronavirus Infections/virology , Disease Models, Animal , Endotoxemia/chemically induced , Female , Immunologic Factors/administration & dosage , Immunologic Factors/chemistry , Lipopolysaccharides/pharmacology , Male , Mice , Mice, Inbred BALB C , Mice, Inbred C57BL , Nanoparticles/administration & dosage , Pandemics , Pneumonia, Viral/drug therapy , Pneumonia, Viral/pathology , Pneumonia, Viral/virology , SARS-CoV-2 , Squalene/administration & dosage , Systemic Inflammatory Response Syndrome/chemically induced , Treatment Outcome , alpha-Tocopherol/administration & dosage , alpha-Tocopherol/chemistry
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