The use of remdesivir to treat COVID-19 will likely continue before clinical trials are completed. Due to the lengthening pandemic and evolving nature of the virus, predicting potential residues prone to mutation is crucial for the management of remdesivir resistance. Using a rational ligand-based interface design complemented with mutational mapping, we generated a total of 100,000 mutations and provided insight into the functional outcomes of mutations in the remdesivir-binding site in nsp12 subunit of RdRp. After designing 46 residues in the remdesivir-binding site of nsp12, the designs retained 97%-98% sequence identity, suggesting that very few mutations in nsp12 are required for SARS-CoV-2 to attain remdesivir resistance. Several mutants displayed decreased binding affinity to remdesivir, suggesting drug resistance. These hotspot residues had a higher probability of undergoing selective mutation and thus conferring remdesivir resistance. Identifying the potential residues prone to mutation improves our understanding of SARS-CoV-2 drug resistance and COVID-19 pathogenesis.
Isocitrate lyase (ICL), a potential anti-tubercular drug target, catalyzes the first step of the glyoxylate shunt. In the present investigation, we studied the conformational flexibility of MtbICL to better understand its stability and catalytic activity. Our biochemical results showed that a point mutation at Phe345, which is topologically distant (>10 Å) to the active site signature sequence (189KKCGH193), completely abolishes the activity of the enzyme. In depth computational analyses were carried out for understanding the structural alterations using molecular dynamics, time-dependent secondary structure and principal component analysis. The results showed that the mutated residue increased the structural flexibility and induced conformational changes near the active site (residues 170–210) and in the C-terminal lid region (residues 411–428). Both these regions are involved in the catalytic activity of MtbICL. Upon mutation, the residual mobility of the enzyme increased, resulting in a decrease in the stability, which was confirmed by the lower free energy of stabilization in the mutant enzyme suggesting the destabilization in the structure. Our results have both biological importance and chemical novelty. It reveals internal dynamics of the enzyme structure and also suggests that regions other than the active site should be exploited for targeting MtbICL inhibition and development of novel anti-tuberculosis compounds.
Fascioliasis, a neglected foodborne disease caused by liver flukes
(genus Fasciola), affects more than 200 million people
worldwide. Despite technological advances, little is known about the
molecular biology and biochemistry of these flukes. We present the
draft genome of Fasciola gigantica for
the first time. The assembled draft genome has a size of ∼1.04
Gb with an N50 and N90 of 129 and 149 kb, respectively. A total of
20 858 genes were predicted. The de novo repeats
identified in the draft genome were 46.85%. The pathway included all
of the genes of glycolysis, Krebs cycle, and fatty acid metabolism
but lacked the key genes of the fatty acid biosynthesis pathway. This
indicates that the fatty acid required for survival of the fluke may
be acquired from the host bile. It may be hypothesized that the relatively
larger F. gigantica genome did not
evolve through genome duplications but rather is interspersed with
many repetitive elements. The genomic information will provide a comprehensive
resource to facilitate the development of novel interventions for
fascioliasis control.
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