Development of peptide nucleic acid antibiotics

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The world is rapidly heading towards a pre-1940’s scenario when it comes to fighting infectious disease. Antimicrobial resistance is a growing problem on a global scale, greatly hampering our abilities to quell worldwide epidemics such as influenza, SARS, COVID-19, tuberculosis and malaria, as well as the simple staphylococcus infection. Unless innovative strategies are developed to produce robust and effective new classes of antibiotics, health care costs will continue to climb and we will completely lose our ability to combat even the most common infection. Influenza and coronavirus (SARS and COVID-19) create an even more urgent need for targeting resistant bacteria related to lung infections, such as carbapenem-resistant Enterobacteriaceae (CRE), a common example of CRE being Klebsiella Pneumoniae (KP). Recent article by J. Gerberding, former CDC director states “The patients at greatest risk from superbugs like CRE and other bacterial pathogens that cause lung diseases, are the ones who are already more vulnerable to illness from viral lung infections like influenza, severe acute respiratory syndrome (SARS), and COVID-19. The 2009 H1N1 influenza pandemic, for example, claimed nearly 300,000 lives around the world. Many of those deaths — between 29% and 55% — were actually caused by secondary bacterial pneumonia, according to the CDC.” A recent study (Zhou, Lancet 2020, 395, 1054-1062) from Wuhan reports that almost 50% of COVID-19 related deaths showed evidence of secondary bacterial infections (pneumonia, sepsis, bloodstream infections). Cases of multidrug-resistant (MDR, resistance to 2-3 classes), extensive drug resistance (XDR, resistance to most classes except colistin or tigecycline) and even pan drug resistance (PDR, resistance to all classes) nosocomial bacterial infections have skyrocketed in recent years, and the emergence of pan drug-resistant isolates are making these infections increasingly difficult to treat. Hospital-acquired infections like these account for up to 4% of all hospital stays in the United States and are incredibly diverse in causative pathogen, antibiotic resistance profile, and severity. A significant cause of nosocomial infection is the Enterobacteriaceae family, which includes Gram-negative bacilli that can be commensal or pathogenic. Enterobacteriaceae have a widespread clinical and economic impact due to the diversity of infections they cause; this family causes many infections such as pneumonia, bloodstream infections (BSIs), urinary tract infections (UTIs), and intra-abdominal infections (IAIs). The World Health Organization (WHO) lists carbapenem-resistant Enterobacteriaceae (CRE) as having a critical need for novel antibiotics on their Priority Pathogens list. Because the mortality of these multi drug-resistant infections is between 30 and 50% and there is such difficulty in finding viable treatments, the need for novel therapeutics for these pathogens must be addressed. One of the challenges of research in infectious diseases is to find ways to use the increasing knowledge of the mechanisms underlying disease biology, transformation and progression to develop novel therapeutic strategies targeting MDR, XDR, and PDR bacterial infections. Targeting heavily conserved RNA sequences and structures, present in the 4 billion years old bacterial ribosome, and involved in proliferation and survival of bacteria, is a promising approach. RNA, the essential nucleic acid component of the ribosome, is a validated target for drug design, both as therapeutic and as a target. We will target specific rRNA single strands, which are conserved across prokaryotes, essential for translation initiation but absent in eukaryotes, ensuring that a drug targeting this sequence can function as a broad spectrum therapeutic. In the proposed work, we will construct sequence- specific chemically modified rRNA targeting oligomers that can be effectively delivered inside the cell. Short RNA will be exploited as target for synthetic molecules that inactivate the functioning of the ribosome, stopping bacterial protein synthesis and causing bacterial death. NUBAD’s unique experimental approaches and technologies will allow us to target rRNA combinations not previously explored for susceptibility against bacteria. The work proposed is a multidisciplinary effort encompassing solid-phase organic synthesis, oligonucleotide stability and delivery, RNA targeted screening, antimicrobial activity, ADME TOX, and in vivo efficacy studies describes the development of sequence-specific cell permeable binders of rRNA. The success of the proposed work would be a significant addition to currently available ribosome-specific approaches in drug development. We propose using a small rRNA target sequence, heavily conserved in prokaryotes, to design conjugates that can be employed to inhibit microbial growth, opening possibilities for developing sequence-specific RNA targeted therapeutics. This work addresses an important world health issue, antimicrobial resistance, and presents creative steps towards a novel solution to this problem.