Discussion
First, our findings show that similar intracellular concentrations of
remdesivir relative to dATP can effectively inhibit SARS-CoV2
replication. Indeed, Gordon et al. reported high selectivity of the
antiviral over incorporation of dATP using purified active RdRp-CoV2
[12]. Further,
remdesivir has been reported to inhibit SARS-CoV-2 in lung cells at
submicromolar concentrations in vitro
[22]. Moreover, similar
binding site for remdesivir in the SARS-CoV-2 polymerase have been
reported recently by two different approaches, based on a 3D-structural
alignment using other virus polymerases
[23] and a constrained
minimization and conformational search on the RdRp-CoV2 active site
[22,23]. In fact,
our model provided the specific molecular interactions supporting the
binding site (see supplementary material S3 for detailed description).
The cyano group in remdesivir, a group not present in the other ligands,
allows additional H-bond interactions with the nascent RNA chain, likely
being the cause for the strongest ΔGbinding. In sum, our
findings on the remdesivir-SARS-CoV2 interaction are robustly aligned
with recent studies and validates our approach as a reliable framework
to evaluate nucleic acids analogues against SARS-CoV2. We conclude that
the partial clinical efficacy observed for remdesivir is not the result
of molecular interactions with the RdRp-CoV2, given its strong binding
affinity and drug target stability. Alternatively, remdesivir
effectiveness might rely on unstudied pharmacokinetic properties and/or
time to treatment relative to viral replication.
Regarding tenofovir, our approach is the first to include
template-nascent RNA in the ensemble and further improves previous work
[24] by using cryo-EM
structures instead of homology and by more extensive sampling of the
ligand poses using volunteer distributed computations. Consistent with
our findings, tenofovir-diphosphate has been shown to permanently
terminate polymerase extension of nascent RNA when using recombinant
RdRp-CoV2 [25]. However,
infusion of tenofovir in Vero cell cultures did not inhibit replication
of SARS-CoV-2
[26,27], while the
use of 3-90 μM of its prodrug TDF yielded a 15-fold reduction of viral
genome release [26] .
Further, the use of TDF/FTC for treating SARS-CoV-2 infected ferrets led
to better clinical scores and lower virus titers in nasal washes
compared to a placebo
[28]. Worth noting, the
prodrug TDF, formulated to increase tenofovir limited bioavailability
[29], is known to
diffuse passively across cellular membranes
[30,31] and further
activate intracellularly, as opposed to tenofovir which requires active
transportation for intake before activation
[32,33]. Indeed,
higher levels of active metabolite after exposure to TDF versus
tenofovir has been consistently reported in several cell types
[34–36]. In
contrast, the prodrug TAF was formulated to reduce drug-adverse events
observed for TDF (which distributes body-wide) by being highly
HIV-target-cell specific. TAF is well known to selectively activate and
present preferential distribution in lymphatic tissues
[37].
Our findings support a suboptimal tenofovir-RdRp-CoV2 interaction
compared to remdesivir, predicting that the ensemble is more sensitive
to the triphosphate form intracellular concentration. Thus, matching
sufficient intracellular availability of tenofovir-diphostate with
SARS-CoV2 tropism
[37,38](such as in
the respiratory tract
[39]) is essential in
drug-driven containment of viral replication, mirroring HIV prophylaxis
[35]. Of note, viral
replication can occur in different tissues at different clinical stages
[40]. Thus, tenofovir
efficacy might highly depend on when it is given relative to the
within-host SARS-CoV-2 distribution. Together with the available
pharmacokinetic/pharmacodynamic evidence, our findings support that TDF,
among tenofovir-based compounds, maximizes efficacy at safe clinical
dosage especially when taken before or close after exposure, because of
high cellular permeation, effective metabolite activation, and
low-selective distribution at viral targeted tissues, laying out a
plausible molecular interpretation of the apparent inconsistency of
tenofovir-based compounds against SARS-CoV-2
[11]. Finally, our
findings support further evaluation of remdesivir as treatment against
COVID-19 but also for the prodrug TDF
[10] (available as a
generic worldwide), in particular as prophylaxis, while underscoring the
need for understanding the intracellular availability of the drugs in
SARS-CoV2 targeted tissues.