Analysis of bacterial Mur amide ligase enzymes for the identification of inhibitory compounds by in silico methods
- Authors: Chamboko, Chiratidzo Respina
- Date: 2020
- Subjects: Mur amide ligases , Ligases , Ligand binding (Biochemistry) , Antibacterial agents
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/163430 , vital:41036
- Description: An increased emergence of resistant pathogenic bacterial strains over the years has resulted in many people dying of untreatable infections. This has become one of the most critical global public health problems, as resistant strains are complicating treatment of infectious diseases, increasing human morbidity, mortality, and health care costs. A very limited amount of effective antibiotics is currently available, but the development of novel classes of antibacterial agents is becoming a priority. Mur amide ligases are enzymes that have been identified as potentially good targets for antibiotics, as they are uniquely found in bacteria. They are responsible for the formation of peptide bonds in a growing peptidoglycan structure for bacterial cell walls. The current work presented here focused on characterizing these Mur amide ligase enzymes and obtaining inhibitory compounds that could potentially be of use in drug discovery of antibacterial agents. To do this, multiple sequence alignment, motif analysis and phylogenetic tree constructions were carried out, followed by docking studies and molecular dynamic simulations. Prior to docking, homology modelling of missing residues in the MurF structure (PDB 1GG4) was performed. Characterization results revealed the Mur amide ligase enzymes contained defined conservation in limited regions, that ultimately mapped towards the central domain responsible for ATP binding (presence of a conserved GKT motif). Further analysis of results further unraveled the unique patterns observed within each group of the family of enzymes. As a result of these findings, docking studies were carried out on each Mur amide ligase structure. At most, two ligands were identified to be sufficiently inhibiting each Mur amide ligase. The ligands obtained were SANC00574 and SANC00575 for MurC, SANC00290 and SANC00438 for MurD, SANC00290 and SANC00525 for MurE and SANC00290 and SANC00434 for MurF. The two best ligands identified for each enzyme had docked in the active site of their respective proteins, passed Lipinski’s rule of five and had substantially low binding energies. Molecular dynamic simulations were then performed to analyze the behavior of the proteins and protein-ligand complexes, to confirm the lead compounds as good inhibitors of the Mur amide ligases. In the case of MurC, MurD and MurE complexes, the identified ligands clearly impacted the behavior of the protein, as the ligand bound proteins became more compact and stable, while flexibility decreased. There was however an opposite effect on MurF complexes, that resulted in identified inhibitors being discarded. As a potential next step, in vivo and in vitro experiments can be performed with identified ligands from this research, to further support the information presented.
- Full Text:
- Date Issued: 2020
Extraction, isolation and characterization of oleanolic acid and its analogues from Syzygium aromaticum (cloves) and evaluation of their biological activities
- Authors: khwaza, Vuyolwethu
- Date: 2019
- Subjects: Antibacterial agents
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/19076 , vital:39882
- Description: Pathogenic microorganisms have serious impact on people's lives. Every year, millions of people around the world die of bacterial infections. Resistance to common antibacterial drugs has proven to be a challenging problem in control of bacterial infections. In an attempt to develop an effective and affordable treatment for bacterial infections, oleanolic acid isolated from syzygium aromaticum conjugates incorporating other pharmaceutical scaffolds such as chloroquine derivatives, curcumin, and ergocalciferol etc have been developed. Based on the previous successes of testing combination of antimicrobial drugs and pharmaceutical drugs which appeared to be the promising strategy to overcome treatment failure; a series of hybrid compounds containing oleanolic acid and other pharmaceutical scaffolds were synthesized. 4- Aminoquinoline derivatives were first hybridized with selected organic compounds to form a class of hybrid compounds containing either amide bond or ester bond as a linker between the precursor molecules. Analogues/hybrid compounds can overcome the disadvantages of combination therapy such as drug-drug interaction. The structural effects of this type of conjugation of oleanolic acid and other pharmaceutical scaffolds were characterised by FTIR, Mass Spec and NMR spectroscopy. These compounds were studied along with the monosubstituted oleanolic acid analogues and the organic components in order to compare the effects of the substitution on their biological response.‖ All the synthesized analogues were tested against 11 bacterial strains on both Gram-positive and Gram-negative bacteria. The synthesized compounds showed selectivity and higher activity against Enterococcus faecalis (EF), Klebsiella oxytoca (KO), Escherischia coli (EC), Staphylococcus aureous (SA), Proteus vulgaris (PV) and Bacillus subtilis (BS) with MIC values; ranging between of 1.25 mg/mL to 0.072 mg/mL
- Full Text:
- Date Issued: 2019
Antibacterial activities of both combined and individual medicinal plants extracts traditionally used to treat pneumonia
- Authors: Mhango, Immaculate
- Date: 2017
- Subjects: Antibacterial agents , Pneumonia -- Treatment
- Language: English
- Type: Thesis , Masters , MA
- Identifier: http://hdl.handle.net/10948/19762 , vital:28959
- Description: Pneumonia is one of the five major leading causes of death in children under-fives years and the elderly worldwide. Antibiotics used for its treatment are less potent due to bacteria development of bacteria resistant to antibiotics. This has led to a surge in search of novel drugs. There are already some drugs in clinical use that have natural products and derivatives such as quinine, morphine, vincristine, and taxol among others. The healing value of medicinal plants has been well accepted since Stone Age across the globe. This plant therapy has been prescribed and prepared independently or in combination. The following plants: Terminalia sericea, Warburgia salutaris, Dodonea angustofolia, Eucalyptus camaldulensis, Ballota africana, Kigelia africana and Acorus gramineus. These plants are most commonly used for treatment of pneumonia and other ailment, were studied to validate their antimicrobial activity based on scientific determination. The primary aim of this study was to evaluate the efficacy of these plants against bacteria pneumonia pathogens. Seven medicinal plants, independently and in combinations were relatively analysed for their antimicrobial activity against Staphylococcus aureus, Streptococcus pyogenes, and Klebsiella pneumoniae. Ground plant material of roots, bark and leafs were prepared with acetone, ethanol and distilled water. Dimethyl sulfoxide (10 &100%) was used as a reconstitution solvent and ciprofloxacin (10 %) as a positive control. The antimicrobial efficacy was determined using agar well diffusion and microtiter plate methods. Interaction between plants was evaluated by calculating fraction inhibitory concentration index (ΣFIC). Noteworthy activity for individual studies with all test organisms was observed with T. sericea. However, highest ZOI (30 mm) was observed for B. africana ethanol extract for S. pyogenes. Weak microbial activity was noted in W. salutaris and D. angustofolia extracts with all test organisms. Good antimicrobial activity was observed in combination studies with all organisms. The potency of different plant combinations varied with highest ZOI observed with B. africana and W. salutaris ranging from 33-35 mm, conversely ZOI of 35 mm was also noted for S. aureus in B. africana and E. camaldulensis ethanol extract. Noteworthy antimicrobial activity was observed in T. sericea and D. angustofolia against all test pathogens. weak antimicrobial activity with highest MICs was observed in combinations where W. salutaris was involved. After calculating ΣFICs, strongest synergistic effect was displayed for W. salutaris and D. angustofolia against all test organisms (lowest ΣFICs 0.0491). Most plant extract combinations, displayed either synergistic, additive or indifferent effect, with few demonstrating antagonistic interactions. Significant antagonism effect was noted for S. pyogenes with T. sericea ethanol extract ΣFIC value of 15.51. Based on results of this study use of plants in combination increase antimicrobial efficacy. The antimicrobial activities; synergistic and additive effects observed adds credibility in the use of plant combination for therapeutic value in treatment of pneumonia. Future studies are recommended to identify and isolate specific active compounds involved in plant combination interactions. The importance of combination studies for possible development of new antimicrobials that can succumb bacterial resistance need to be highlighted.
- Full Text:
- Date Issued: 2017