Rational design of Gram-negative active S-MGBs using Whole Genome Bind-n-Seq

Urgent action is needed to develop novel antimicrobials to treat multidrug resistant (MDR) bacterial infections. The 2014 O'Neill report suggests that, without action, the annual number of deaths from antimicrobial resistant infections will be 10 million by 2050, costing 100 trillion USD globally. Of particular concern is the lack of novel compounds for the treatment of Gram-negative pathogens, which are especially challenging because it is difficult for drugs to penetrate the Gram-negative bacterial cell envelope. Our research is focussed on a class of compounds called Strathclyde Minor Groove Binders (S-MGBs). The structure of S-MGBs is based upon the natural product, distamycin, which acts as an antibacterial by binding to, and inhibiting, DNA gyrase. S-MGBs have structural similarity to distamycin but they have a novel mode of action.
Project Aims:
To date, no methodology has been developed that can comprehensively map the minor groove binding landscape of S-MGBs across whole genomes nor in high-throughput. Whole genome bind-n-seq will not only facilitate profiling S-MGB-DNA binding interactions but it could also be used as a valuable tool to rapidly optimize their drug-like properties and efficacy using Structure Activity Relationship (SAR) paradigms. Specifically, this will aid the development of S-MGBs with significant activity against Gram-negative organisms.
The aim of this proposal is to integrate a systems biology approach into a drug discovery platform in order to expedite the rational design and targeting of Strathclyde Minor Groove Binder therapeutics. The novelty of this work arises from the ability of our methods to map DNA-binding across the genome of the target organism using a suite of deep sequencing methodologies. Whole genome bind-n-seq represents a platform technology that can be used to tune and optimise DNA-binding drugs to precisely target DNA sequences with high selectivity.
In summary, successful development of bind-n-seq into our drug development programme will expedite the optimization of new antibiotics suitable for pre-clinical evaluation. Importantly, once this approach has been established for our S-MGB platform, we will be able to apply it to the design of anti-viral and anti-parasitic S-MGBs, significantly expanding the impact of this work.

Objectives:
The ultimate aim is to demonstrate the feasibility of bind-n-seq to interrogate the DNA binding profile of S-MGBs in Gram-positive and Gram-negative genomes thereby enabling the development of novel S-MGBs into pre-clinical evaluation. This method provides the foundations of a new systems biology-directed approach to targeting the design of MGBs in a high-throughput fashion. Our objectives are:
1. To synthesise tagged S-MGBs suitable for "bind-n-seq" technology.
2. To apply "bind-n-seq" methodology using MGBs prepared in Objective 1.
3. To iterative synthesis of S-MGBs that are active against Gram-negative bacteria.