Insights Into Mutations Induced Conformational Changes and Rearrangement of Fe2+ Ion in pncA Gene of Mycobacterium tuberculosis to Decipher the Mechanism of Resistance to Pyrazinamide

Abstract

Pyrazinamide (PZA) is the first-line drug commonly used in treating Mycobacterium tuberculosis (Mtb) infections and reduces treatment time by 33%. This prodrug is activated and converted to an active form, Pyrazinoic acid (POA), by Pyrazinamidase (PZase) enzyme. Mtb resistance to PZA is the outcome of mutations frequently reported in pncA, rpsA, and panD genes. Among the mentioned genes, pncA mutations contribute to 72–99% of the total resistance to PZA. Thus, considering the vital importance of this gene in PZA resistance, its frequent mutations (D49N, Y64S, W68G, and F94A) were investigated through in-depth computational techniques to put conclusions that might be useful for new scaffolds design or structure optimization to improve the efficacy of the available drugs. Mutants and wild type PZase were used in extensive and long-run molecular dynamics simulations in triplicate to disclose the resistance mechanism induced by the above-mentioned point mutations. Our analysis suggests that these mutations alter the internal dynamics of PZase and hinder the correct orientation of PZA to the enzyme. Consequently, the PZA has a low binding energy score with the mutants compared with the wild type PZase. These mutations were also reported to affect the binding of Fe2+ ion and its coordinated residues. Conformational dynamics also revealed that β-strand two is flipped, which is significant in Fe2+ binding. MM-GBSA analysis confirmed that these mutations significantly decreased the binding of PZA. In conclusion, these mutations cause conformation alterations and deformities that lead to PZA resistance.

In silico protein engineering shows that novel mutations affecting NAD+ binding sites may improve phosphite dehydrogenase stability and activity

“…The 3D structure of PTDH (accession ID: 4E5N) was retrieved from the PDB databank 14 . The water molecules were eliminated from the protein file before starting downstream analyses 15 . Chimera v1.14 was used to inspect the structure for any fractures or missing residues.…”

Drug-target genes and their spontaneous mutations associated with resistance to first-line, second-line, third-line, novel and repurposed anti-tuberculosis drugs in Mycobacterium tuberculosis resistant strains

“…Mutations in the pncA, panD, rpsA, clpC1(Rv3596c), and Rv2783c genes of MTB confer resistance to pyranamide (PZA). 22,29,40,54 However, mutations in the pncA and its promoter region are the most frequently identified as they account for 72-99% of resistance to PZA. 22,54 The most frequent mutations in the pncA gene are: Asp49Asn, Tyr64Ser, Trp68Gly, and Phe94Ala.…”

“…22,29,40,54 However, mutations in the pncA and its promoter region are the most frequently identified as they account for 72-99% of resistance to PZA. 22,54 The most frequent mutations in the pncA gene are: Asp49Asn, Tyr64Ser, Trp68Gly, and Phe94Ala. 54 Studies have also shown that PZA resistance is strongly associated with rifampicin resistance.…”

“…22,54 The most frequent mutations in the pncA gene are: Asp49Asn, Tyr64Ser, Trp68Gly, and Phe94Ala. 54 Studies have also shown that PZA resistance is strongly associated with rifampicin resistance. This finding confirms that the burden of PZA resistance is in patients who have rifampicin resistance.…”

Computational discovery of binding mode of anti-TRBC1 antibody and predicted key amino acids of TRBC1

“…These methods were proven to be successful in various molecular predictions such as drug-protein complexes 9 – 11 and antibody design 12 , 13 . Molecular docking was generally used to generate the possible pose for the molecular binding between two entities based on docking score namely relative free binding energy or other ranking score types 14 , 15 , meanwhile, molecular dynamics simulation can fulfill the simulated effects due to surroundings such as temperature, pressure, solution ionic strength 11 , 16 , 17 , or even membrane environment 18 , 19 . In this study, we have performed computational modeling of TRBC1 and TRBC2 under dynamics conditions to visualize the effect of alternated Asn-Lys on the protein structure.…”