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Hydroxychloroquine and the Coronavirus: Connecting the Dots Through the Biology Knowledge Graph

Posted on April 16th, 2020 by in COVID-19

It would be hard to miss the current interest in finding effective treatment for COVID-19. In this regard, the combination of hydroxychloroquine (HCQ) with azithromycin is getting a great deal of attention. HCQ, sold under the brand name Plaquenil, is a well-known anti-malarial drug, while azithromycin is a common antibiotic that is usually used for the treatment of strep throat (the widely used Zithromax, Z-Pak).

Quinine (CQ), extracted from the bark of the cinchona trees found in the tropical Andean forests of western South America, was widely used in the 19th century to treat malaria infections that commonly arise in the tropics. The synthetically produced derivative drugs of quinine, chloroquine and the more recently produced hydroxychloroquine, are widely used to prevent and treat malaria but also used off-label for the treatment of rheumatoid arthritis and lupus.

A small clinical trial conducted in the south of France produced encouraging results on the use of the hydroxychloroquine and azithromycin combination for the treatment of COVID-19 [4]. This was further supported by preliminary experiments showing the ability of CQ and HCQ to inhibit SARS-CoV-2 activity in vitro [1, 2]. In addition to these published data, there is a large amount of anecdotal data from frontline physicians treating COVID-19 in New York and California, who are enthusiastic about the responses they have gotten using combinations of HCQ, azithromycin and zinc.

However, Dr. Anthony Fauci, Director of the National Institute of Allergy and Infectious Diseases (NIAID), points out that this type of real-world data cannot substitute for large-scale randomized clinical trials for determining the safety and efficacy of COVID-19 treatments. Such trials take into account the detailed parameters of the patient population, try to determine the stage of the viral infection at which the treatment should be initiated, identify unexpected adverse events that might be associated with the regimen in the population, and follow up with patients to determine the long-term effects of the treatment. But trials with such measures can’t be done properly under the current time pressure we are facing during the COVID-19 outbreak. Nevertheless, in recognition of the current state of emergency, treatment guidelines have already incorporated the usage of chloroquine/hydroxychloroquine for certain patients with COVID-19 in the US.

Until finding the best bioethical approach (as an alternative to randomized clinical trials) that can be performed under such circumstances, we thought that it would be helpful to determine the interactions of these drugs with key proinflammatory proteins related to Acute Respiratory Distress Syndrome (ARDS).

Similar to our previous analysis of analgesics and ARDS, we aimed to identify the effects of hydroxychloroquine, chloroquine and azithromycin on proteins known to be up-regulated by severe ARDS using Elsevier’s Biology Knowledge Graph.

Interestingly, chloroquine could inhibit 10/20 and activate 3/20 of ARDS-induced proteins, while hydroxychloroquine could inhibit 11/20, with no detectable activation, of ARDS-induced proteins (Figure 1).

Figure 1. Chloroquine and Hydroxychloroquine inhibit ARDS activated
proteins, yellow = inhibited proteins, green = activated proteins.

Then, we compared the overall effects of these drugs on ARDS-induced proteins with those of non-steroidal anti-inflammatory (NSAID) drugs from our previous analysis (analgesics and ARDS). The complete results are shown in Table 1. Ascorbic acid (vitamin C), a nutraceutical, and aspirin, a common analgesic, were the strongest inhibitors based on their overall relationship with ARDS-induced proteins (Table 1A).

Table 1. The effects of drugs of interest on ARDS-induced proteins. Drugs sorted left to right from strongest inhibitors to strongest activators based on (A) the overall relationship with ARDS proteins, or (B) the total number of relevant references.

In contrast, similar to our previous analysis, acetaminophen was the strongest activator of ARDS-induced proteins. On the other hand, chloroquine and aspirin were the two strongest inhibitors when looking at the total number of references supporting a particular drug’s profile of activity on all the ARDS-induced proteins. This could be related to the fact that these two drugs have been studied more extensively compared to the other drugs. Interestingly, azithromycin moved up the list of inhibitors in Table 1B, suggesting a large literature around the interaction between this drug and ARDS proteins.

ARDS is a characteristic of the late stages of an unresolved coronavirus infection, namely Stage III or Hyperinflammation Phase (Figure 2).

Figure 2. COVID-19 Disease Stages and Potential Therapeutic Treatments.
The figure comes from Mehra et al and shows three escalating stages of COVID-19 disease progression, with the associated signs, symptoms and potential stage-specific therapies. ARDS = Acute respiratory distress syndrome; CRP = C-reactive protein; IL = Interleukin; JAK = Janus Kinase; LDH=Lactate Dehydrogenase; SIRS = Systemic inflammatory response syndrome. [3]

Hence, it occurred to us to identify the direct effects of HCQ and azithromycin on the core proteins of hyperinflammation. These proteins include major inflammatory response mediators such as the neutrophil chemoattractant CXCL8; immunoregulatory cytokines such as IL1B, IL2, IL4, IL6 and IL10; the proinflammatory protein TNF; the mediator of cellular response to viral infections IFNG; and the cytotoxicity signaling molecule IL12. Together these proteins can initiate and control both acute and chronic inflammation.

Figure 3. HCQ alone inhibits all of the core proteins of hyperinflammation (red and yellow highlights), while azithromycin inhibits 5/9 of the core proteins (red highlights only).

The results represented in Figure 3 suggest that both HCQ and azithromycin can exert an overall inhibitory effect on the core proteins of hyperinflammation. Despite the need for further validation, these results strongly indicate a major immunosuppressant role for both drugs on hyperinflammation. This may suggest their restrictive administration only to hospitalized patients despite previous recommendations that they might also be used for the treatment of prophylaxis. Interestingly, a similar mechanism of action by chloroquine on viral infections has been proposed previously. [5]

Examination of the references supporting the above network offered a curious observation regarding the inhibition of CXCL8 by azithromycin. As noted above, CXCL8 functions as a chemoattractant for neutrophils. Airway infiltration by neutrophils can result in severe lung damage and is the leading cause of death after lung transplantation. In this regard, azithromycin was previously shown to reduce airway neutrophilia and interleukin-8 levels in patients with bronchiolitis obliterans syndrome, a common transplantation complication, as well as it significantly increased the expression of FEV(1), a positive indicator of lung function. [6]

However, the authors were unable to identify the exact mechanism of action in their study. Why would a high-grade antibiotic improve lung function? An open question that, similar to many other tantalizing clues regarding possible COVD-19 treatments, was once forgotten and now has been revived again.

Please feel free to contact me or my colleague Chris Cheadle if you are interested in all this data and the manually curated COVID-19 pathways.

And as for hydroxychloroquine and azithromycin, will they live up to their promise? Until a concrete answer is available, we will continue to expand our knowledge-based database and contribute to the current knowledge on COVID-19.


1.         Gao, J.J., Z.X. Tian, and X. Yang, Breakthrough: Chloroquine phosphate has shown apparent efficacy in treatment of COVID-19 associated pneumonia in clinical studies. Bioscience Trends, 2020. 14(1): p. 72-73.

2.         Yao, X., et al., In Vitro Antiviral Activity and Projection of Optimized Dosing Design of Hydroxychloroquine for the Treatment of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Clin Infect Dis, 2020.

3.         Sidiqi, H.K. and M.R. Mehra, COVID-19 Illness in Native and Immunosuppressed States: A Clinical-Therapeutic Staging Proposal. J Heart Lung Transplant, 2020.

4.         Gautret, P., et al., Hydroxychloroquine and azithromycin as a treatment of COVID-19: results of an open-label non-randomized clinical trial. Int J Antimicrob Agents, 2020: p. 105949.

5.         Savarino, A., et al., Effects of chloroquine on viral infections: an old drug against today’s diseases? Lancet Infect Dis, 2003. 3(11): p. 722-7.

6.         Verleden, G.M., et al., Azithromycin reduces airway neutrophilia and interleukin-8 in patients with bronchiolitis obliterans syndrome. American Journal of Respiratory and Critical Care Medicine, 2006. 174(5): p. 566-570.

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