title: A report of rifampin-resistant leprosy from northern and eastern India: identification and in silico analysis of molecular interactions.
abstract: Presence of point mutations within the drug resistance determining regions of Mycobacterium leprae (M. leprae) genome confers molecular basis of drug resistance to dapsone, rifampin and ofloxacin in leprosy. This study is focused on the identification of mutations within the rpoB gene region of M. leprae that are specific for rifampin interaction, and further in silico analysis was carried out to determine the variations in the interactions. DNA and RNA were isolated from slit skin scrapings of 60 relapsed leprosy patients. PCR targeting rpoB gene region and amplicon sequencing was performed to determine point mutations. mRNA expression levels of rpoB and high-resolution melt analysis of mutants were performed using Rotor Gene Q Realtime PCR. Molecular docking was performed using LigandFit Software. Ten cases having point mutations within the rpoB gene region were identified and were clinically confirmed to be resistant to rifampin. A new mutation at codon position Gln442His has been identified. There is a 9.44-fold upregulation in the mRNA expression of rpoB gene in mutant/resistant samples when compared with the wild/sensitive samples. In silico docking analysis of rifampin with wild-type and Gln442His mutant RpoB proteins revealed a variation in the hydrogen-bonding pattern leading to a difference in the total interaction energy and conformational change at position Asp441. These preliminary downstream functional observations revealed that the presence of point mutations within the rifampin resistance determining regions of rpoB gene plays a vital role in conferring genetic and molecular basis of resistance to rifampin in leprosy.
authors.affiliation: Stanley Browne Laboratory, The Leprosy Mission Community Hospital, Nand Nagri, New Delhi, 110093, India, sundeepchaitanya@gmail.com.
authors.forename: Sundeep Chaitanya
authors.initials: SC
authors.lastname: Vedithi
authors.forename: Mallika
authors.initials: M
authors.lastname: Lavania
authors.forename: Manoj
authors.initials: M
authors.lastname: Kumar
authors.forename: Punit
authors.initials: P
authors.lastname: Kaur
authors.forename: Ravindra P
authors.initials: RP
authors.lastname: Turankar
authors.forename: Itu
authors.initials: I
authors.lastname: Singh
authors.forename: Astha
authors.initials: A
authors.lastname: Nigam
authors.forename: Utpal
authors.initials: U
authors.lastname: Sengupta
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D019295:Computational Biology; D004269:DNA, Bacterial / Q000235:genetics / Q000302:isolation & purification; D012321:DNA-Directed RNA Polymerases / Q000235:genetics; D024881:Drug Resistance, Bacterial; D005260:Female; D020869:Gene Expression Profiling; D006801:Humans; D007194:India / Q000453:epidemiology; D007918:Leprosy / Q000453:epidemiology* / Q000382:microbiology*; D008297:Male; D008875:Middle Aged; D062105:Molecular Docking Simulation; D008969:Molecular Sequence Data; D009166:Mycobacterium leprae / Q000187:drug effects* / Q000302:isolation & purification; D017354:Point Mutation; D016133:Polymerase Chain Reaction; D012333:RNA, Messenger / Q000032:analysis; D012293:Rifampin / Q000494:pharmacology*; D017422:Sequence Analysis, DNA; D055815:Young Adult
chemical_list: D000900:Anti-Bacterial Agents; D004269:DNA, Bacterial; D012333:RNA, Messenger; D012321:DNA-Directed RNA Polymerases; C105078:RNA polymerase beta subunit; D012293:Rifampin