The current COVID-19 outbreak warrants the design and development of novel anti-COVID therapeutics. Using a combination of bioinformatics and computational tools, we modelled the 3D structure of the RdRp (RNA-dependent RNA polymerase) of SARS-CoV2 (severe acute respiratory syndrome coronavirus-2) and predicted its probable GTP binding pocket in the active site. GTP is crucial for the formation of the initiation complex during RNA replication. This site was computationally targeted using a number of small molecule inhibitors of the hepatitis C RNA polymerase reported previously. Further optimizations suggested a lead molecule that may prove fruitful in the development of potent inhibitors against the RdRp of SARS-CoV2.

Transketolase is a connecting link between glycolytic and pentose phosphate pathway, which is considered as the rate-limiting step due to synthesis of large number of ATP molecule and it can be proposed as a plausible target facilitating the growth of cancerous cells suggesting its potential role in cancer. Oxythiamine, an antimetabolite has been proved to be an efficient anticancerous compound in vitro, but its structural elucidation of the inhibitory mechanism has not yet been done against the human transketolase-like 1 protein (TKTL1). The three-dimensional (3D) structure of TKTL1 protein was modeled and subjected for refinement, stability and validation. Based on the reported homologs of transketolase (TKT), the active site residues His46, Ser49, Ser52, Ser53, Ile56, Leu82, Lys84, Leu123, Ser125, Glu128, Asp154, His160, Thr216 and Lys218 were identified and considered for molecular-modeling studies. Docking studies reveal the H-bond interactions with residues Ser49 and Lys218 that could play a major role in the activity of TKTL1. Molecular dynamics (MD) simulation study was performed to reveal the comparative stability of both native and complex forms of TKTL1. MD trajectory at 30 ns, confirm the role of active site residues Ser49, Lys84, Glu128, His160 and Lys218 in suppressing the activity of TKTL1. Glu128 is observed to be the most important residue for deprotonation state of the aminopyrimidine moiety and preferred to be the site of inhibitory action. Thus, the proposed mechanism of inhibition through in silico studies would pave the way for structure-oriented drug designing against cancer.

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In this study, the binding recognition and allosteric mechanism of tryptophan-responsive regulatory protein (TRP)–DNA and bound exogenous tryptophan (Trp) amino acid complexes for transcriptional regulation were explained through the molecular docking, molecular dynamics (MD), free-energy landscape (FEL), binding free energy (molecular mechanics Poisson–Boltzmann surface area, MMPBSA), and protein structural network (PSN) analyses. The domain transition of helix–turn–helix (HTH) and effector binding domain (EBD) of TRP protein is the vital process for allosteric network communication, DNA recognition, and transcription. TRP protein consists of four putative active site pockets (Act1, Act2, Act3, and Act4) with the binding specificity of exogenous Trp amino acid, which modulates the binding energy of TRP–DNA complexes by conferring the specific residual network and internal helical orientation of DNA-binding domain (DBD) for regulatory mechanism. In the TRP–DNA complex, interaction of Arg28 (helix-1) and Arg36 (helix-2) with the DNA molecule plays a vital role in DNA recognition. As a consequence, allosteric induction of exogenous Trp in the Act3 binding site retains the structural integrity and is quite comfortable with DNA major groove; therefore, it produces less binding energy for complex formation and may involve in oligomeric association for transcription regulation. Meanwhile, Trp in the Act1 binding site induces high helical orientation and fluctuations, leading to dissociation of DNA from the TRP protein. The remaining two complexes of Trp with Act2 and Act4 are predicted to partially affect the transcription mechanism. The present study aims to unravel the role of exogenous Trp amino acid in TRP protein for transcriptional regulatory mechanism.

Apart from the canonical fingers, palm and thumb domains, the RNA dependent RNA polymerases (RdRp) from the viral order Nidovirales possess two additional domains. Of these, the function of the Nidovirus RdRp associated nucleotidyl transferase domain (NiRAN) remains unanswered. The elucidation of the 3D structure of RdRp from the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), provided the first ever insights into the domain organisation and possible functional characteristics of the NiRAN domain. Using in silico tools, we predict that the NiRAN domain assumes a kinase or phosphotransferase like fold and binds nucleoside triphosphates at its proposed active site. Additionally, using molecular docking we have predicted the binding of three widely used kinase inhibitors and five well characterized anti-microbial compounds at the NiRAN domain active site along with their drug-likeliness. For the first time ever, using basic biochemical tools, this study shows the presence of a kinase like activity exhibited by the SARS-CoV-2 RdRp. Interestingly, a well-known kinase inhibitor- Sorafenib showed a significant inhibition and dampened viral load in SARS-CoV-2 infected cells. In line with the current global COVID-19 pandemic urgency and the emergence of newer strains with significantly higher infectivity, this study provides a new anti-SARS-CoV-2 drug target and potential lead compounds for drug repurposing against SARS-CoV-2.

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