Natural compounds showing exquisite binding to monomeric and homo-dimeric structures of histone like DNA binding protein of <i>Helicobacter pylori </i>(Hup) identified through molecular docking and molecular dynamics studies
Creators: name: Kumar, Dinesh
Publisher: name: F1000 Research Limited
Year: 2018

description: <i>Helicobacter pylori</i> (<i>H. pylori</i>) –a human gastric pathogen colonizing more than 50% of the world’s population- is responsible for several human gastric pathologies such as inflammatory gastritis, peptic ulcer disease, and gastric cancer. It is now well established that its eradication greatly reduces the recurrence rate of gastric pathologies involving <i>H. pylori</i> infection [1,2]. Worldwide, the first line standard treatment used to eradicate <i>H. pylori</i> infection involves two/three antibiotics and a proton pump inhibitor (PPi) or a bismuth compound, termed triple/quadruple therapy [3].  However, <i>H. pylori</i> eradication rates with triple/quadruple therapy have significantly decreased, varying from 60 to 75%, as a result of an increase in the emergence of <i>H. pylori</i> strains with primary or acquired resistance to current arsenal of antimicrobials [2,4,5]. This emergence of antibiotic resistance can be explained by the indiscriminate use of antibiotics or noncompliance with treatment regimens or the development of resistance during treatment of other previous infections with broad-spectrum antibiotics [2,4,5]. Further to achieve complete <i>H. pylori</i> eradication, the medication is generally prescribed for 10-14 days, which can cause severe side effects in some cases [2,6]. This makes the pathogenic potential of this microorganism a major global health concern and has emphasized urgent need to develop novel anti-<i>H. pylori</i> agents with both superior therapeutic efficacy and negligible side effects.<br><br>In the above context, <i>H. pylori</i> Hup protein (homologous to histone-like-DNA-binding protein HU of <i>Escherichia coli</i>) has been recognized as a potential drug target owing to its role in protecting <i>H. pylori</i> genomic DNA from damage elicited by extreme acidic and oxidative stress conditions, that the bacterium encounters under host gastric environment [7-9]. Physiologically, the protein (with 94 amino acid sequence) predominantly exists as a homo-dimer in solution [10,11]. The homodimeric Hup interacts with different (single/double stranded) DNA structures  in a non-sequence specific manner  to regulate vital DNA transactions such as replication, recombination, repair, and transcription [12,13]. Under acidic stress conditions, the protein possibly undergoes conformational changes and participates in DNA compaction; thus prevents its denaturation [7,11,14]; whereas oxidative stress possibly provokes different kinds of conformational changes in Hup (owing to oxidation of its side chains) and participate in <i>oxidative stress</i> management through modulating gene expressions. Overall, the protein contributes to <i>H. pylori</i> survival and persistent colonization under harsh gastric conditions which is the combined effect due to its roles in DNA-protection (physically), recombination/repair events, and modulation of gene-expression in response to acidic/oxidative stress conditions [7-9]. Although Hup is crucial for <i>H. pylori </i>survival, there have been no reported attempts to perturb its functioning with small molecules. The small molecule inhibitors can be identified in a timely and cost-effective manner following rational structure-based drug discovery (SBDD) approach which involves virtual screening of ligand databases [15,16]. The approach requires atomic level understanding of protein structure and mechanism of its interaction with its physiological binding partners; where it is protein-protein and protein-DNA interaction in the present context. To that end, we overexpressed the recombinant Hup protein and studied its structural, dynamics and DNA binding features under near physiological conditions [11]. The study revealed the occurrence of dynamic equilibrium between its monomer and dimer conformations and the equilibrium was found to shifting towards dimer at low temperature as well as at low pH. The DNA binding studies evidenced that the DNA binds to homodimeric Hup structure. These findings correlated very well with the diverse functionality of protein and formed the basis for future studies aiming to develop novel anti‐<i>H. pylori</i> agents. As a next step in this direction, we screened here a compound library of natural products and identified potential hit compounds which were subsequently evaluated for their stable and reliable binding to Hup through molecular dynamics simulations. The preliminary results and their future perspectives have been presented in the poster.<br> <br>References:<br>            [1]        A. R. Gaby, Helicobacter pylori eradication: are there alternatives to antibiotics?, Alternative Medicine Review, 6 (2001) 355-366.<br><br>            [2]        A. J. Alanis, Resistance to antibiotics: are we in the post-antibiotic era?, Archives of medical research, 36 (2005) 697-705.<br><br>            [3]        R. Urgesi, R. Cianci, and M. E. Riccioni, Update on triple therapy for eradication of Helicobacter pylori: current status of the art, Clinical and experimental gastroenterology, 5 (2012) 151.<br><br>            [4]        E. A. Cameron and Co-workers , <i>Helicobacter pylori</i>: antibiotic resistance and eradication rates in Suffolk, UK, 1991-2001, J Med. Microbiol, 53 (2004) 535-538.<br><br>            [5]        F. Megraud, H pylori antibiotic resistance: prevalence, importance, and advances in testing, Gut, 53 (2004) 1374-1384.<br><br>            [6]        B. V. Bonifácio, M. A. dos Santos Ramos, P. B. da Silva, and T. M. Bauab, Antimicrobial activity of natural products against Helicobacter pylori: a review, Annals of clinical microbiology and antimicrobials, 13 (2014) 54.<br><br>            [7]        G. Wang, L. F. Lo, and R. J. Maier, A histone-like protein of Helicobacter pylori protects DNA from stress damage and aids host colonization, DNA Repair (Amst), 11 (2012) 733-740.<br><br>            [8]        M. J. Duckworth, A. S. Okoli, and G. L. Mendz, Novel Helicobacter pylori therapeutic targets: the unusual suspects, Expert. Rev Anti. Infect. Ther., 7 (2009) 835-867.<br><br>            [9]        C. Chen, S. Ghosh, and A. Grove, Substrate specificity of Helicobacter pylori histone-like HU protein is determined by insufficient stabilization of DNA flexure points, Biochem. J., 383 (2004) 343-351.<br>            [10]      NCBI Reference Seqeunce: https://www.ncbi.nlm.nih.gov/protein/WP_001029082.1.<br><br>            [11]      N. Jaiswal and Co-workers, NMR Elucidation of Monomer-dimer transition and Conformational heterogeneity in Histone-like DNA binding protein of Helicobacter pylori (Hup), Magn. Reson. Chem, 56 (2018) 285-299.<br><br>            [12]      D. Kamashev and Co-workers , Comparison of histone-like HU protein DNA-binding properties and HU/IHF protein sequence alignment, PloS one, 12 (2017) e0188037.<br><br>            [13]      D. Kamashev and J. Rouviere-Yaniv, The histone-like protein HU binds specifically to DNA recombination and repair intermediates, EMBO. J, 19 (2000) 6527-6535.<br><br>            [14]      A. Grove, Functional evolution of bacterial histone-like HU proteins, Current issues in molecular biology, 13 (2011) 1-12.<br><br>            [15]      VYAS V, JAIN A, JAIN A, and Gupta A. Virtual Screening : A Fast Tool for Drug Design. Sci.Pharm. 76[3], 333-360. 2008.<br><br>            [16]      S. Mandal, M. Moudgil, and S. K. Mandal, Rational drug design, Eur. J Pharmacol., 625 (2009) 90-100.