Manipal School of Life Sciences
Antibiotics are natural products that are produced by microorganisms and act against other microbes. A few entirely synthetic molecules have been developed and are also referred to here as antibiotics. To improve solubility, potency, and pharmacokinetics and to evade resistance mechanism, antibiotic molecules were chemically modified. These modifications can be done depending on the structural knowledge of the drug bound to the active site.
Antimicrobial resistance is an alarming situation around the globe from the past decade, with the development of new multitude mechanisms in overcoming the drug effects and surviving on its exposure. This has led to prevention in the treatment of diseases caused by different microorganisms such as bacteria, viruses, parasites, and fungi. ESKAPE is the acronym widely used to refer multidrug resistant and virulent pathogens including Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. Continuous antibiotics usage has led to drug resistance, which makes drugs ineffective. Hence, there is extensive therapeutic need to treat infections caused by ESKAPE pathogens. This resistance to the drugs can be achieved in two ways, including mutations in the genes or through horizontal gene transfer, i.e., receiving new genes from any other bacteria. Few of these random or specific mutations make the bacteria resistant against antimicrobials.
Taking an example of Staphylococcus aureus, a Gram-negative pathogen, non-spore forming and belonging to Micrococcaceae family. Methicillin-resistant S. aureus (MRSA) strains were first proposed in 1961 and are altered by penicillin-binding protein (PBP2a/c) which are resistant to penicillins, cephalosporins, and carbapenems. Penicillin-binding proteins were seen to be effective as they make the β-lactam armamentarium ineffective. S. aureus is responsible for many diseases including skin infections, osteomyelitis, endocarditis, necrotizing pneumonia, and sepsis. Whole genome sequencing of MRSA revealed that S. aureus is composed of numerous genes obtained by lateral transfer and these drug resistance genes are usually found in the plasmids or resistance islands.Population of infectious organisms is comprised of 40-50% of this pathogen. MRSA caused highest number of infections cases in the United States leading to 10,600 deaths in the year 2017. S.aureus enter the host cells and proliferate, creating many small-colony variants (SCV).
These variants have become more tolerant to antibiotic therapy by reducing its own metabolic activity. In one of the studies, point mutations in PBP 2 gene were compared among the MRSA strains and it was found that the binding of penicillin drug to these strains was altered, indicating a reduced binding affinity leading to the release of the bound drug. These structural and biochemical changes are responsible for the resistance of the strains to β-lactam antibiotics.
Acinetobacter baumannii, another multidrug-resistant pathogen, has created an emergency health threat situation worldwide due to its rapid spreading. Through complete genome analysis by next-generation sequencing, it was found that drug resistant genes were acquired during a bacterial infection. There are various genomic islands known as resistance islands interspersed on the genome carrying resistance elements responsible for developing resistance to multiple drugs. Hence, this dynamic genome organization facilitates the pathogen to acquire drug-resistance elements.
The effect of variations can be studied by performing molecular docking for normal and mutant targets. Mutations are identified in different targets sequences which are used to perform docking with a known antibiotic, binding to a known binding pocket. Binding energy, pockets, and interactions are analysed to check for the effect of mutations in the drug binding which is causing drug-resistance in the pathogenic microorganisms. Analysing the mutations and genome organization of bacteria can help understand the impact of the genetic variations on the development of drug resistance and their molecular mechanisms.