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Projects / Programmes source: ARIS

Exploitation of a virus-borne small protein to combat antibiotic resistance in Staphylococcus aureus

Research activity

Code Science Field Subfield
4.06.04  Biotechnical sciences  Biotechnology  Microbe biotechnology 

Code Science Field
T490  Technological sciences  Biotechnology 

Code Science Field
3.04  Medical and Health Sciences  Medical biotechnology 
Keywords
antibiotics, antibiotic-resistance, virtual screening for inhibitors, antibiotic adjuvant, Staphyylococcus aureus, bacteriophage, SOS response
Evaluation (rules)
source: COBISS
Researchers (22)
no. Code Name and surname Research area Role Period No. of publicationsNo. of publications
1.  24290  PhD Matej Butala  Biochemistry and molecular biology  Head  2019 - 2022  237 
2.  53672  Sandra Cetin  Pharmacy  Researcher  2021 
3.  23399  PhD Tomaž Curk  Computer science and informatics  Researcher  2019 - 2022  254 
4.  15284  PhD Stanislav Gobec  Pharmacy  Researcher  2019 - 2022  849 
5.  35424  PhD Tomaž Hočevar  Computer science and informatics  Researcher  2019 - 2022  30 
6.  53283  Maja Hostnik  Biochemistry and molecular biology  Researcher  2020 - 2022  19 
7.  52386  Eva Kočar  Biochemistry and molecular biology  Technical associate  2019 - 2020  30 
8.  25435  PhD Janez Konc  Computer intensive methods and applications  Researcher  2019  236 
9.  55572  PhD Alen Krajnc  Pharmacy  Researcher  2022  34 
10.  00412  PhD Igor Križaj  Biochemistry and molecular biology  Researcher  2019 - 2022  736 
11.  53699  Amela Kujović  Biochemistry and molecular biology  Technical associate  2019 - 2020  26 
12.  18802  PhD Adrijana Leonardi  Biochemistry and molecular biology  Researcher  2019 - 2022  161 
13.  39099  PhD Katja Molan  Biochemistry and molecular biology  Junior researcher  2019  44 
14.  55449  Martina Mravinec  Biochemistry and molecular biology  Researcher  2021  11 
15.  39090  PhD Anastasija Panevska  Biochemistry and molecular biology  Researcher  2019 - 2021  57 
16.  51231  PhD Anja Pavlin  Biochemistry and molecular biology  Junior researcher  2019 - 2022  26 
17.  06902  PhD Zdravko Podlesek  Biochemistry and molecular biology  Researcher  2020 - 2022  137 
18.  52376  PhD Matic Proj  Pharmacy  Junior researcher  2019 - 2022  67 
19.  04570  PhD Jože Pungerčar  Biochemistry and molecular biology  Researcher  2019 - 2022  320 
20.  15328  PhD Kristina Sepčić  Biochemistry and molecular biology  Researcher  2019 - 2021  741 
21.  52378  Nika Strašek Benedik  Pharmacy  Junior researcher  2020 - 2022  30 
22.  21553  PhD Jernej Šribar  Biochemistry and molecular biology  Researcher  2019 - 2022  110 
Organisations (4)
no. Code Research organisation City Registration number No. of publicationsNo. of publications
1.  0481  University of Ljubljana, Biotechnical Faculty  Ljubljana  1626914  67,273 
2.  0106  Jožef Stefan Institute  Ljubljana  5051606000  91,971 
3.  0787  University of Ljubljana, Faculty of Pharmacy  Ljubljana  1626973  17,415 
4.  1539  University of Ljubljana, Faculty of Computer and Information Science  Ljubljana  1627023  16,709 
Abstract
The development of drug‑resistant bacteria is an unavoidable outcome of widespread antibacterial chemotherapy of infectious diseases. Drug discovery programs directed against proteins considered essential for in vivo bacterial viability have yielded few new therapeutic classes of antibiotics, therefore treatment options for combating bacteria resistant to multiple drugs are narrowing. Hence, novel strategies to fight bacterial pathogens are urgently needed. Adaptation of bacteria to antibiotic therapy requires specific biochemical processes that may be subject to intervention. Preventing bacteria to acquire resistance to antibiotics will significantly prolong the lifetime of current‑day antibiotics. We will achieve this by an innovative strategy, with novel drugs that block antibiotic stress and resistance development in bacteria, prolonging the efficacy of licensed antibiotics. Clinically significant antibiotics induce mechanisms in pathogenic bacteria that activate the DNA damage response, designated the SOS response. Antibiotic‑induced SOS responses can (i) modulate the evolution and spread of drug resistance as well as virulence factors in pathogens, (ii) induce mutations and generate antibiotic resistance during therapy, (iii) induce persistence and multidrug tolerance in a subpopulation of bacterial cells that are not heritably resistant, (iv) induce biofilm formation and (v) toxin synthesis. The importance of regulating responses to stress suggests that modulation of SOS induction has the potential to address the problem of evolution of antibiotic resistance at its roots. Experimentally inactivating transcription factor LexA, the key regulator of the response, renders the bacteria unable to initiate the SOS response, these strains are sensitized to genotoxic antimicrobials and exhibit decreased mutation rates. The natural products synthesized by microorganisms are privileged compounds for the discovery of antibiotics as they result from natural selection and are the source of highly effective antibiotics. Our recent results reported the discovery of a small, 50-residue bacteriophage protein, gp7, able to interact with and modulate functions of the global transcription factor LexA, a key SOS regulator involved in the development of antibiotic resistance. This is the first report of a natural molecule that interacts directly with LexA to inhibit its self-cleavage activity and enhance its DNA binding, thus inhibit the host SOS response. We obtained the crystal structure of the gp7 protein and according to SAXS data we generated a structural model of gp7 in complex with LexA. Based on the unpublished structures we aim to obtain few high-affinity LexA-inhibitory lead compounds or gp7 derivatives, that will after optimisation give rise to a safe “anti-evolutionary” therapeutics, to be used in combination with licensed antibiotics to fight Bacillus sp. and Staphlococcus aureus infections. First we will enhance our knowledge on biology of gp7 protein in vitro and on the genome-wide scale in Bacillus and Staphylococcus sp. This will enable us to better understand gp7-driven processes in the cell which is essential to be able to generate a safe anti-evolutionary therapeutics. Next, we will use computer-assisted drug design based on the gp7 protein characteristics to select for the chemical libraries which will be assayed for the Bacillus sp. and the S. aureus LexA self-cleavage inhibitors. This will provide us with lead SOS inhibitor structures to block mechanisms enabling resistance. We will determine the equilibrium dissociation constants for the leads-LexA interaction and evaluate the antibiotic-potentiated activity of molecules targeting LexA by assaying the inhibition of the antibiotic resistance accumulation in Bacillus sp. and in S. aureus. We believe that optimised leads/gp7-derivatives in combination with current‑day, licensed antibiotics will assist in the battle against the development of antibiotic resistance by ba
Significance for science
World Health Organisation called for an urgent and concerted action: »Combat drug resistance: no action today means no cure tomorrow.« We need to bring new classes of antibiotics to market to prevent people from dying from infections that have been treatable for decades, until resistance rendered our drugs ineffective. An academic-industry parthership has just few months ago reported the first LexA-targeting small molecules. Given the fact that GlaxoSmithKline entered such collaborative effort that lead to the identification of first-in-class inhibitors of LexA self-cleavage confirms the importance of recognising LexA as a novel, potent antibacterial drug target to address the rising tide of antibiotic resistance bacteria. However, they used an approach in which they targeted the LexA self-cleavage reaction. They observed that by hitting directly the catalytic domain of LexA makes it a difficult target for competitive inhibiton, given the high local concentration of the cleavage loop »substrate« around the LexA active site. Thus, only after refeiment of the certain chemotype targeting LexA the authors (their article has been just accepted) could  reach the IC50 value down to 9 µM for the E. coli LexA. This indicates, that although great effort was allready invested, even further optimisation is needed which might result in an efficient inhibitor. Here we propose a different and unique approach based on the natural gp7 protein characteristics and on our unpublished structural LexA-gp7 insight. We will design an effective allosteric inhibitors of LexA that we predict will target at least LexA of Bacillus sp. and S. aureus. Our approach is novel in that gp7 will be used as a scafold to design gp7 derivatives or small lead molecules that stabilize LexA in a DNA bound conformation and additionaly orient LexA cleavage site loop in the non-clavable state, thus firmly inhibiting repressors`s self-cleavage by precluding LexA to interact with RecA. It is of note that we have previously shown that gp7 inhibits LexA to interact with RecA and that DNA bound LexA cannot be inactivated. Thus, here we offer a promissing novel approach to design unique drugs that block antibiotic stress and resistance development in bacteria, prolonging the efficiency of licensed antibiotics. In addition, we want to elucidate gp7 effect on processes in B. thuringiensis and S. aureus on the genome wide-scale. This is important to understand the gp7-effects in vivo and the results will surely be of great interest to the broad scientific commnity. In E. coli, ChIP-chip approach revealed that an additional factor is required for LexA binding to noncanonical sites in vivo (Wade et al., Genes Dev. 2005). Thus, we strongly believe that gp7-like LexA effectors exist also in other bacteria which could provide scafolds for potent drugs against antibiotic-resitance development in selected pathogens. Thus, our project proposal may open up a novel class of tomorrow`s antibacterials.
Significance for the country
World Health Organisation called for an urgent and concerted action: »Combat drug resistance: no action today means no cure tomorrow.« We need to bring new classes of antibiotics to market to prevent people from dying from infections that have been treatable for decades, until resistance rendered our drugs ineffective. An academic-industry parthership has just few months ago reported the first LexA-targeting small molecules. Given the fact that GlaxoSmithKline entered such collaborative effort that lead to the identification of first-in-class inhibitors of LexA self-cleavage confirms the importance of recognising LexA as a novel, potent antibacterial drug target to address the rising tide of antibiotic resistance bacteria. However, they used an approach in which they targeted the LexA self-cleavage reaction. They observed that by hitting directly the catalytic domain of LexA makes it a difficult target for competitive inhibiton, given the high local concentration of the cleavage loop »substrate« around the LexA active site. Thus, only after refeiment of the certain chemotype targeting LexA the authors (their article has been just accepted) could  reach the IC50 value down to 9 µM for the E. coli LexA. This indicates, that although great effort was allready invested, even further optimisation is needed which might result in an efficient inhibitor. Here we propose a different and unique approach based on the natural gp7 protein characteristics and on our unpublished structural LexA-gp7 insight. We will design an effective allosteric inhibitors of LexA that we predict will target at least LexA of Bacillus sp. and S. aureus. Our approach is novel in that gp7 will be used as a scafold to design gp7 derivatives or small lead molecules that stabilize LexA in a DNA bound conformation and additionaly orient LexA cleavage site loop in the non-clavable state, thus firmly inhibiting repressors`s self-cleavage by precluding LexA to interact with RecA. It is of note that we have previously shown that gp7 inhibits LexA to interact with RecA and that DNA bound LexA cannot be inactivated. Thus, here we offer a promissing novel approach to design unique drugs that block antibiotic stress and resistance development in bacteria, prolonging the efficiency of licensed antibiotics. In addition, we want to elucidate gp7 effect on processes in B. thuringiensis and S. aureus on the genome wide-scale. This is important to understand the gp7-effects in vivo and the results will surely be of great interest to the broad scientific commnity. In E. coli, ChIP-chip approach revealed that an additional factor is required for LexA binding to noncanonical sites in vivo (Wade et al., Genes Dev. 2005). Thus, we strongly believe that gp7-like LexA effectors exist also in other bacteria which could provide scafolds for potent drugs against antibiotic-resitance development in selected pathogens. Thus, our project proposal may open up a novel class of tomorrow`s antibacterials.
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