COVID-19: Mechanisms of the Antiviral Activities of Selective Antibiotics Targeting the Human 80S Ribosome

Background:

The majority of scientists, physicians, and healthcare professionals were trained with the paradigm: “antibiotics are for bacteria only !”, because they misunderstood the definition of the ribosome targeting antibiotics. In the context of the current worldwide COVID-19 pandemic, it might be useful to recall as precisely as possible the definition of the word antibiotic and provide evidence that some classes of antibiotics could offer excellent means to counteract viral infections via specific mechanisms.

Methods:

Molecular modeling and docking studies were used, as well as the tRNAox labeling reaction of the ribosomal protein eL42 in situ on human 80S ribosomes to demonstrate that cycloheximide and its thiosemicarbazone analogues bind to the catalytic Lys-53 residue of the human large subunit ribosomal protein eL42.

Results:

Comparison of the binding sites for Cycloheximide (CHX) and Sparsomycin (SPS) on the evolutionarily conserved E. coli bL12 and S. cerevisiae eL42 by means of molecular modeling and docking studies showed that: (i) SPS binds in proximity to the catalytic Lys-65 residue of the GANK motif of rp bL12 and to the catalytic Lys-55 residue of the GGQTKP motif of rp eL42; (ii) CHX failed to bind to the GANK motif, while the glutarimide moiety of SPS and CHX was found to make contact with Lys-55 of the GGQTKP motif of rp eL42.

Conclusion:

In this report, we demonstrate that cycloheximide and its thiosemicarbazone analogues are capable of inhibiting the human 80S ribosomes selectively through their binding to the ε-amino group of the side chain of Lys-53. As a consequence, these small-molecule inhibitors of translation are susceptible to exhibit antiviral activities by preventing the human ribosomes of the SARS-CoV-2 infected cells from synthesizing the viral proteins and enzymes.

Repositioning Adequate Antibiotics to Treat/Cure the Coronavirus Disease 2019 (COVID-19): Current Treatments and Future Directions

Aims:

Rational use of antibiotics against the betacoronavirus SARS-CoV-2 responsible for the COVID-19 pandemic.

Objective:

Repositioning and repurposing adequate antibiotics to cure the Coronavirus Disease 2019 (COVID-19).

Background:

It is widely accepted that viral infections such as the SARS-CoV-2 cannot be cured by antibiotics, whereas bacterial infections can. It is because the SARS-CoV-2 virus has no protein synthesis machinery (usually targeted by antibiotics) to produce from its RNA genome, the viral proteins and enzymes essential for its replication and/or for the assembly of viral particles. However, the antibiotics must be capable of inhibiting the ribosomes of the protein synthesis machinery of the SARS-CoV-2-infected human host cells, in order to prevent them from synthesizing new proteins that they do not need, but are needed for the virus to spread. Unfortunately, the only antibiotic capable of selectively inhibiting the human 80S ribosomes, namely cycloheximide, was found to be a poisonous drug for the mammals. Therefore, the only possibility is to search for the antibiotics that are capable of inhibiting both bacterial and eukaryal ribosomes, in order to prevent at the same time the ribosomes of the infected human host cells from synthesizing the proteins and enzymes for the SARS-CoV-2 virus, and those of the eventual opportunistic pathogenic bacteria from developing pneumonia.

Methods:

First, we have used a molecular modeling study involving the tools of the semi-empirical quantum mechanics PM3 method to study the interaction between the cation Zn++ and all the molecules considered as zinc transporters in this report. By this approach, the niche in which Zn++ is located was determined. Such an interaction serves as a shuttle and allows zinc cation to invade endocellular structures in the SARS-CoV-2-infected human host cells. Second, we have measured the poly (U)-dependent poly (Phe) synthesis activity of human 80S ribosomes in the presence of increasing concentrations of four antibiotics of the class of the macrolides, namely erythromycin, azithromycin, clarithromycin and telithromycin. This experiment led us to determine for each macrolide, the half-inhibitory concentration (IC50) that is the concentration of antibiotic corresponding to 50% inhibition of the activity of the human 80S ribosomes. Finally, we have analyzed previously published data from the group of Nierhaus (Berlin) on the competition between the incoming aminoacyl-tRNA and the antibiotic tetracycline for the binding to the ribosomal A-site on the E. coli 70S or rabbit liver 80S ribosomes. This led to the conclusion by the authors that tetracycline most likely binds to corresponding sites in 70S and 80S ribosomes with comparable affinity.

Results:

We propose to reposition the macrolides (azithromycin or erythromycin or others) and tetracyclines for the treatment of COVID-19 patients, on account of the following data gathered in this report. First, these antibiotics are already currently successfully used in medicine in humans and animals. Second, the binding sites of these antibiotics at the upper part of the protein exit tunnel (for the macrolides) and the ribosomal A-site (for tetracyclines) are universally conserved features of the ribosomes in all kingdoms of life. So, these classes of antibiotics are expected to bind to all kinds of ribosomes, the 70S as well as the 80S type, with comparable affinity. Therefore, they are capable of preventing at the same time the ribosomes of the infected human host cells from synthesizing the proteins and enzymes for the SARS-CoV-2 virus, and those of the eventual opportunistic pathogenic bacteria from developing pneumonia. Third, the efficacy assessment of these antibiotics in clinical application consisted of comparing their affinity constants of binding to the human ribosomes with their blood concentration.

For example, in the case of azithromycin, the amount of antibiotic administered to COVID-19 patients was 100 μg/ml of circulating blood, which is 43 times superior to the half-inhibitory concentration (IC50 or KIa of 2.3 μg/ml), the concentration of azithromycin corresponding to 50% inhibition of the activity of the human 80S ribosomes. Fourth, zinc cations were previously shown to be a strong antiviral agent, while all the macrolides and tetracyclines that we propose for repurposing or repositioning to cure the COVID-19 are shown in the present report to form Zn++-antibiotic complex and behave as efficient zinc transporters into the SARS-CoV-2-infected host cells.

Conclusion:

The macrolides (azithromycin or erythromycin or others) and tetracyclines selected for repositioning and repurposing to cure COVID-19 are candidates as specific and effective therapeutic drugs available for the coronavirus disease. We propose to combat the current COVID-19 pandemic with azithromycin or erythromycin (or equivalent) alone or in combination with tetracycline (or equivalent) in the presence of Zn++(SO4--). Taking into account the fact that azithromycin had been shown to be effective in treating viral infections such as papillomaviruses in humans and dogs, we conclude that the statement “no antibiotic for viral infections !” is not relevant for all the clinically approved classes of antibiotics, because selective antibiotics such as the universal antibiotics described in the present report are capable of exhibiting antiviral activities through specific interactions with the human 80S ribosomes of infected host cells. As a conclusion, even though the clinical and experimental data presented here do not suggest virucidal activity of azithromycin-zinc or tetracycline-zinc complexes, they do indicate that when administered simultaneously at the onset of first signs of COVID-19, the most common symptoms being fatigue, fever, dry cough, headache, sore throat, muscle pain or shortness of breath, azithromycin (or tetracycline) and zinc cations are capable of inhibiting ribosomal activity of SARS-CoV-2-infected human cells. This results in blocking protein and enzyme synthesis vital for viral RNA replication and for assembly of viral particles. Early treatment allows both reductions of viremia as well as stabilizing symptoms. The major advantage of this therapeutic strategy is avoiding prolonged clinical COVID-19 disease with contingent worsening of illness and subsequent need for intensive care. Prolonged COVID-19 illness is the major downfall of the present pandemic, returning to normal being long, difficult, and sometimes impossible.

In Vitro Analysis of Protein:Protein Interactions in the Human Cancer-Pertinent rp.eL42-p53-Mdm2 Pathway

Introduction:

We have recently demonstrated that the eukaryote-specific large subunit ribosomal protein (rp) eL42 assists catalysis of peptide bond formation at the peptidyl transferase center of 80S ribosomes in eukaryotic cells. Recently, several ribosomal proteins were shown to have extraribosomal functions independent of protein biosynthesis. Such functions include regulation of apoptosis, cell cycle arrest, cell proliferation, neoplastic transformation, cell migration and invasion, and tumorigenesis through both Mdm2-p53-dependent and p53-independent mechanisms. Our objective is to demonstrate that overexpression of eL42 in tumor may incapacitate cell anti-tumor mechanism through interaction with the tumor suppressor protein p53 and its partner Mdm2.

Methods:

Co-immunoprecipitation technique and the binding assays on Biacore were used to probe interactions between recombinant eL42, p53 and Mdm2 proteins in a so-called rp-p53-Mdm2 axis.

Results:

We demonstrate that the ribosomal protein eL42, the tumor suppressor protein p53 and the ubiquitin E3 ligase Mdm2 interact with each other in a ternary rp.eL42:p53:Mdm2 complex. Precisely, the interaction between eL42 and p53 is characterized by a strong binding affinity (KD value in the nanomolar range) that is likely to trigger the sequestration of p53 and the inhibition of its tumor suppressor activity. Furthermore, the p53:Mdm2 and eL42:Mdm2 complexes exhibit comparable binding affinities in the micromolar range compatible with Mdm2 being the enzyme which ubiquitinates both the p53 and eL42 substrates. Interestingly, pyridoxal 5'-phosphate (PLP), one of the active forms of vitamin B6, binds to eL42 and significantly inhibits the interaction between eL42 and p53, in accordance with the observation that vitamin B6 is associated with reduced risk of cancer.

Conclusion:

Our study emphasized one more major mechanism of p53 downregulation involving its sequestration by eL42 upon the overexpression of this ribosomal protein. The mechanism described in the present report complemented the well-known p53 downregulation triggered by proteasomal degradation mediated through its ubiquitination by Mdm2.

Ribosomal protein eL42 contributes to the catalytic activity of the yeast ribosome at the elongation step of translation

The GGQ minidomain of the ribosomal protein eL42 was previously shown to contact the CCA-arm of P-site bound tRNA in human ribosome, indicating a possible involvement of the protein in the catalytic activity. Here, using Schizosaccharomyces pombe (S. pombe) cells, we demonstrate that the GGQ minidomain and neighboring region of eL42 is critical for the ribosomal function. Mutant eL42 proteins containing amino acid substitutions within or adjacent to the GGQ minidomain failed to complement the function of wild-type eL42, and expression of the mutant eL42 proteins led to severe growth defects. These results suggest that the mutations in eL42 interfere with the ribosomal function in vivo. Furthermore, we show that some of the mutations associated with the conserved GGQ region lead to reduced activities in the poly(Phe) synthesis and/or in the peptidyl transferase reaction with respect to puromycin, as compared with those of the wild-type ribosomes. A pK value of 6.95 was measured for the side chain of Lys-55/Arg-55, which is considerably less than that of a Lys or Arg residue. Altogether, our findings suggest that eL42 contributes to the 80S ribosome's peptidyl transferase activity by promoting the course of the elongation cycle.

RpbL12 Assists Catalysis by Correctly Positioning the Incoming Aminoacyl-tRNA in the A-Site of E. coli 70S Ribosomes

Introduction:

We have recently demonstrated that Lys-65 of the 62GANK65 motif of E. coli RpbL12 was affinity labeled with a tRNA analogue, resulting in the loss of activity.

Materials and Methods:

In this report, we show that mutations operated at the position of Lys-65 led to an impairment in the activity of the mutant ribosomes, except the K65R or K65H bL12 mutants, suggesting that the only requirement of the reaction catalyzed or facilitated by RpbL12is the positive charge of the side chain of Lys-65. We also demonstrate that Lys-65 did not play any role in the peptidyl transferase reaction with respect to puromycin, but rather assisted the binding of the incoming aminoacyl-tRNA to the ribosomal A-site.

Results & Discussions

The protonated, positively charged εNH₃⁺ form of Lys-65 is likely to participate to the binding of aa-tRNA through ionic bonds with phosphate groups, in order to insure the accurate positioning required for the nucleophilic attack of its α-amino group on the carbonyl carbone of peptidyl-tRNA.

Conclusion

This α-NH₂ group is likely to be generated by the unprotonated εNH₂ form of Lys-65 which is capable of withdrawing a proton from the α-NH₃⁺ group of aa-tRNA.