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Abera B, Melaku Y, Shenkute K, Degu S, Abebe A, Gemechu W, Endale M, Woldemariam M, Hunsen M, Hussein AA, Dekebo A. In vitro antibacterial and antioxidant activity of flavonoids from the roots of Tephrosia vogelii: a combined experimental and computational study. Z NATURFORSCH C 2024; 0:znc-2024-0044. [PMID: 38865441 DOI: 10.1515/znc-2024-0044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 05/23/2024] [Indexed: 06/14/2024]
Abstract
Tephrosia vogelii is a traditional medicinal plant used to treat hypertension, diarrhea and urinary disorders. Silica gel chromatographic separation of CH2Cl2/MeOH (1:1) roots extract of T. vogelii afforded seven compounds namely; β-sitosterol (1a), stigmasterol (1b), 6a, 12a-dehydro-deguelin (2), tephrosin (3), maackiain (4), obovatin (5) and 6-oxo, 6a, 12a-dehydro-deguelin (6). GC-MS analysis of essential oils from the root of T. vogelii displayed a total of 17 compounds of which cis-nerolidol (41.7 %) and cadinol (19.7 %) were the major constituents. CH2Cl2/MeOH (1:1) extract, MeOH extract, maackiain (4) and obovatin (5) showed moderate inhibitory activity against Pseudomonas aeruginosa with MIC value of 0.5, 0.66, 0.83 and 0.83 mg/mL, respectively, compared to ciprofloxacin (MIC of 0.078 μg/mL). 6a, 12a-dihydro-deguelin (2), and 6-oxo, 6a, 12a-dehydro-deguelin (6) displayed significant activity against S. epidermis with MIC values of 0.66 mg/mL. Tephrosin (3) and maackiain (4) also showed moderate antibacterial activity against Staphylococcus aureus and Proteus mirabilis with MIC values of 0.83 and 0.5 mg/mL, respectively, compared to ciprofloxacin (0.312 μg/mL). The radical scavenging activity results indicated that tephrosin (3), obovatin (5) and 6-oxo, 6a, 12a-dehydro-deguelin (6) showed potent DPPH scavenging activity with IC50 values of 10.97, 10.43 and 10.73 μg/mL, respectively, compared to ascorbic acid (IC50 of 5.83 μg/mL). The docking prediction results revealed that 6a, 12a-dehydro-deguelin (2) displayed the best binding energy of -8.1 kcal/mol towards pyruvate kinase of S. aureus (PDB ID: 3T07) and -7.9 kcal/mol towards P. mirabilis urease (PDB ID: 1E9Y) and DNA gyrase B of Escherichia coli (PDB: 4F86) receptors compared to ciprofloxacin (-7.2 to -8.0 kcal/mol). Maackiain (4) and obovatin (5) displayed the minimum binding energy of -7.9 and -8.2 kcal/mol towards the LasR protein of P. aeruginosa (PDB: ID 2UV) and S. epidermidis FtsZ (PDB: ID 4M8I), respectively. The SwissADME drug-likeness and Pro Tox II toxicity prediction results indicated that compounds (2-6) obeyed Lipinski's rule of five with 0 violations and none of them were found to be hepatotoxic, mutagenic, and cytotoxic, respectively. The in vitro assessment results supported by the in silico analysis revealed that crude extracts and isolated compounds showed promising antibacterial and antioxidant activity, which proves the therapeutic potential of the roots of T. vogelii.
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Affiliation(s)
- Bihon Abera
- Department of Applied Chemistry, 125545 School of Applied Natural Science, Adama Science and Technology University , P.O.Box 1888, Adama, Ethiopia
| | - Yadessa Melaku
- Department of Applied Chemistry, 125545 School of Applied Natural Science, Adama Science and Technology University , P.O.Box 1888, Adama, Ethiopia
| | - Kebede Shenkute
- Department of Applied Chemistry, 125545 School of Applied Natural Science, Adama Science and Technology University , P.O.Box 1888, Adama, Ethiopia
| | - Sileshi Degu
- Traditional and Modern Medicine Research and Development, 70605 Armauer Hansen Research Institute , P.O. Box 1005, Addis Ababa, Ethiopia
| | - Abiy Abebe
- Traditional and Modern Medicine Research and Development, 70605 Armauer Hansen Research Institute , P.O. Box 1005, Addis Ababa, Ethiopia
| | - Worku Gemechu
- Traditional and Modern Medicine Research and Development, 70605 Armauer Hansen Research Institute , P.O. Box 1005, Addis Ababa, Ethiopia
| | - Milkyas Endale
- Traditional and Modern Medicine Research and Development, 70605 Armauer Hansen Research Institute , P.O. Box 1005, Addis Ababa, Ethiopia
| | - Messay Woldemariam
- Pharmaceutical Industry Development, 70605 Armauer Hansen Research Institute , P.O. Box 1005, Addis Ababa, Ethiopia
| | - Mo Hunsen
- Department of Chemistry, 3475 Kenyon College , Gambier, OH 43022, USA
| | - Ahmed A Hussein
- Department of Chemistry, 70683 Cape Peninsula University of Technology , Bellville Campus, 7535, Bellville, Western Cape, South Africa
| | - Aman Dekebo
- Department of Applied Chemistry, 125545 School of Applied Natural Science, Adama Science and Technology University , P.O.Box 1888, Adama, Ethiopia
- 125545 Institute of Pharmaceutical Sciences, Adama Science and Technology University , P.O.Box 1888, Adama, Ethiopia
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2
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Rufer AC. Drug discovery for enzymes. Drug Discov Today 2021; 26:875-886. [PMID: 33454380 DOI: 10.1016/j.drudis.2021.01.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/21/2020] [Accepted: 01/07/2021] [Indexed: 02/06/2023]
Abstract
Enzymes are essential, physiological catalysts involved in all processes of life, including metabolism, cellular signaling and motility, as well as cell growth and division. They are attractive drug targets because of the presence of defined substrate-binding pockets, which can be exploited as binding sites for pharmaceutical enzyme inhibitors. Understanding the reaction mechanisms of enzymes and the molecular mode of action of enzyme inhibitors is indispensable for the discovery and development of potent, efficacious, and safe novel drugs. The combination of classical concepts of enzymology with new experimental and data analysis methods opens new routes for drug discovery.
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Affiliation(s)
- Arne Christian Rufer
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 065/208A, 4070 Basel, Switzerland.
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Abstract
Magnetic particle-based immunoassays are widely used in microbiology-related assays for both microbial capture, separation, analysis, and detection. Besides facilitating sample operation, the implementation of micro-to-nanometer scale magnetic beads as a solid support potentially shortens the incubation time (for magnetic immuno capture) from several hours to less than an hour. Analytical technologies based on magnetic beads offer a rapid, effective and inexpensive way to separate and concentrate the target analytes prior to detection. Magneto-immuno separation uses magnetic particles coated with specific antibodies to capture target microorganisms, bear the corresponding antigens, and subsequently separate them from the sample matrix in a magnetic field. The method has been proven effective in separating various types of pathogenic bacteria from environmental water samples and in eliminating background interferences. Magnetic particles are often used to capture target cells (pathogenic bacteria) from samples. In most commercially available assays, the actual identification and quantitation of the captured cells is then performed by classical microbiological assays. This review highlights the most sensitive analytic methods (i.e., long-range surface plasmon resonance and electrochemical impedance spectroscopy) to detect magnetically tagged bacteria in conjunction with magnetic actuation.
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Affiliation(s)
- Eugen Gheorghiu
- International Centre of Biodynamics, Bucharest 060101, Romania
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Favero LM, Chideroli RT, Ferrari NA, Azevedo VADC, Tiwari S, Lopera-Barrero NM, Pereira UDP. In silico Prediction of New Drug Candidates Against the Multidrug-Resistant and Potentially Zoonotic Fish Pathogen Serotype III Streptococcus agalactiae. Front Genet 2020; 11:1024. [PMID: 33005185 PMCID: PMC7484375 DOI: 10.3389/fgene.2020.01024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 08/11/2020] [Indexed: 12/02/2022] Open
Abstract
Streptococcus agalactiae is an invasive multi-host pathogen that causes invasive diseases mainly in newborns, elderly, and individuals with underlying health complications. In fish, S. agalactiae causes streptococcosis, which is characterized by septicemia and neurological signs, and leads to great economic losses to the fish farming industry worldwide. These bacteria can be classified into different serotypes based on capsular antigens, and into different sequence types (ST) based on multilocus sequence typing (MLST). In 2015, serotype III ST283 was identified to be associated with a foodborne invasive disease in non-pregnant immunocompetent humans in Singapore, and the infection was related to raw fish consumption. In addition, a serotype III strain isolated from tilapia in Brazil has been reported to be resistant to five antibiotic classes. This specific serotype can serve as a reservoir of resistance genes and pose a serious threat to public health. Thus, new approaches for the control and treatment of S. agalactiae infections are needed. In the present study, 24 S. agalactiae serotype III complete genomes, isolated from human and fish hosts, were compared. The core genome was identified, and, using bioinformatics tools and subtractive criteria, five proteins were identified as potential drug targets. Furthermore, 5,008 drug-like natural compounds were virtually screened against the identified targets. The ligands with the best binding properties are suggested for further in vitro and in vivo analysis.
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Affiliation(s)
- Leonardo Mantovani Favero
- Laboratory of Fish Bacteriology, Department of Preventive Veterinary Medicine, State University of Londrina, Londrina, Brazil
| | - Roberta Torres Chideroli
- Laboratory of Fish Bacteriology, Department of Preventive Veterinary Medicine, State University of Londrina, Londrina, Brazil
| | - Natália Amoroso Ferrari
- Laboratory of Fish Bacteriology, Department of Preventive Veterinary Medicine, State University of Londrina, Londrina, Brazil
| | - Vasco Ariston De Carvalho Azevedo
- Institute of Biological Sciences, Department of Genetic, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Sandeep Tiwari
- Institute of Biological Sciences, Department of Genetic, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | | | - Ulisses de Pádua Pereira
- Laboratory of Fish Bacteriology, Department of Preventive Veterinary Medicine, State University of Londrina, Londrina, Brazil
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Abstract
Quantum mechanics (QM) methods provide a fine description of receptor-ligand interactions and of chemical reactions. Their use in drug design and drug discovery is increasing, especially for complex systems including metal ions in the binding sites, for the design of highly selective inhibitors, for the optimization of bi-specific compounds, to understand enzymatic reactions, and for the study of covalent ligands and prodrugs. They are also used for generating molecular descriptors for predictive QSAR/QSPR models and for the parameterization of force fields. Thanks to the continuous increase of computational power offered by GPUs and to the development of sophisticated algorithms, QM methods are becoming part of the standard tools used in computer-aided drug design (CADD). We present the most used QM methods and software packages, and we discuss recent representative applications in drug design and drug discovery.
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Affiliation(s)
- Martin Kotev
- Global Research Informatics/Cheminformatics and Drug Design, Evotec (France) SAS, Toulouse, France
| | - Laurie Sarrat
- Global Research Informatics/Cheminformatics and Drug Design, Evotec (France) SAS, Toulouse, France
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Lu Y, Yuan L, Chen X, Zhang A, Zhang P, Zou D. Systematic analysis and identification of unexpected interactions from the neuroprotein drug interactome in hydrocephalus pharmacological intervention. J Bioinform Comput Biol 2019; 17:1950002. [PMID: 30866733 DOI: 10.1142/s0219720019500021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Hydrocephalus is a neurological condition caused by an abnormal accumulation of cerebrospinal fluid; pharmacological intervention of the disease has been found to elicit a variety of adverse drug reactions (ADRs) in central nervous system (CNS) by unexpectedly targeting certain functional neuroproteins. Here, a systematic neuroprotein drug interactome (SNDI) is created for 11 hydrocephalus drugs/metabolites plus 20 control drugs across 518 druggable pockets on the surface of 472 CNS neuroproteins via a large-scale molecular docking approach. Heuristic clustering analysis of the SNDI profile divides the 31 investigated drug ligands into a distinct panel and a background panel; the former consists of two hydrocephalus drugs (Furosemide and Triamterene) and their respective metabolites (Furosemide glucuronide and Hydroxytriamterene) that are inferred to have generally high affinity towards the whole array of neuroprotein pockets. A total of 13 neuroproteins are enriched in gene ontology semantic mining as putative unexpected targets of the distinct panel, and their intermolecular interactions with hydrocephalus drugs/metabolites are investigated in detail using dynamics simulation and energetics analysis. We also perform kinase assay and viability test to substantiate the interactome analysis. It is found that the Furosemide and Triamterene have significant cytotoxic effects on normal human astrocytes, in which the Triamterene can inhibit the neurokinase ROCK2, a representative of putative unexpected targets, with a high activity, which is comparable with the sophisticated ROCK2 inhibitor Fasudil.
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Affiliation(s)
- Youming Lu
- 1 Department of Neurosurgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, P. R. China
| | - Lei Yuan
- 1 Department of Neurosurgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, P. R. China
| | - Xin Chen
- 1 Department of Neurosurgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, P. R. China
| | - Aijun Zhang
- 1 Department of Neurosurgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, P. R. China
| | - Pengqi Zhang
- 1 Department of Neurosurgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, P. R. China
| | - Dongdong Zou
- 1 Department of Neurosurgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, P. R. China
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Potshangbam AM, Polavarapu R, Rathore RS, Naresh D, Prabhu NP, Potshangbam N, Kumar P, Vindal V. MedPServer: A database for identification of therapeutic targets and novel leads pertaining to natural products. Chem Biol Drug Des 2018; 93:438-446. [PMID: 30381914 DOI: 10.1111/cbdd.13430] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 09/14/2018] [Accepted: 10/18/2018] [Indexed: 12/19/2022]
Abstract
Natural products have been the source of treatment for various human diseases from time immemorial. Interests in natural product-based scaffolds for the discovery of modern drugs have grown in recent years. However, research on exploring the traditional medicinal systems for modern therapeutics is severely limited due to our incomplete understanding of the therapeutic mechanism of action. One possible solution is to develop computational approaches, based on ligand- and structure-based screening tools, for fast and plausible target identification, leading to elucidation of the therapeutic mechanism. In the present work, we present two methods based on shape-based and pharmacophore search to predict targets of natural products and elucidate their mechanism, and to identify natural product-based leads. These methods were tested on an in-house developed database of medicinal plants that include information from a largely unexplored North-East region of India, known as one of the twelve mega biodiversity regions. However, depending on the choice of the lead molecules, any existing databases can be used for screening. MedPServer is an open access resource available at http://bif.uohyd.ac.in/medserver/.
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Affiliation(s)
- Angamba Meetei Potshangbam
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India.,Department of Biotechnology, Manipur University, Imphal, India
| | - Raja Polavarapu
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Ravindranath Singh Rathore
- Bioinformatics Infrastructure Facility, University of Hyderabad, Hyderabad, India.,Department of Bioinformatics, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, India
| | - Damuka Naresh
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Nagu Prakash Prabhu
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | | | - Pravind Kumar
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Vaibhav Vindal
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India.,Bioinformatics Infrastructure Facility, University of Hyderabad, Hyderabad, India
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Liu Q, Li L, Xu F. Systematic analysis and integrative discovery of active-site subpocket-specific dehydroquinate synthase inhibitors combating antibiotic-resistant Staphylococcus aureus infection. J Bioinform Comput Biol 2018; 16:1850027. [PMID: 30567475 DOI: 10.1142/s0219720018500270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Shikimate pathway plays an essential role in the biosynthesis of aromatic amino acids in various plants and bacteria, which consists of seven key enzymes and they are all attractive targets for antibacterial agent development due to their absence in humans. The Staphylococcus aureus dehydroquinate synthase (SaDHQS) is involved in the second step of shikimate pathway, which catalyzes the NAD <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msup><mml:mrow/><mml:mrow><mml:mo>+</mml:mo></mml:mrow></mml:msup></mml:math> -dependent conversion of 3-deoxy-D-arabino-heptulosonate-7-phosphate to dehydroquinate via multiple steps. The enzyme active site can be characterized by two spatially separated subpockets 1 and 2, which represent the reaction center of substrate adduct with NAD <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msup><mml:mrow/><mml:mrow><mml:mo>+</mml:mo></mml:mrow></mml:msup></mml:math> nicotinamide moiety and the assistant binding site of NAD <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msup><mml:mrow/><mml:mrow><mml:mo>+</mml:mo></mml:mrow></mml:msup></mml:math> adenine moiety, respectively. In silico virtual screening is performed against a biogenic compound library to discover SaDHQS subpocket-specific inhibitors, which were then tested against both antibiotic-sensitive and antibiotic-resistant S. aureus strains by using in vitro susceptibility test. The activity profile of hit compounds has no considerable difference between the antibiotic-sensitive and -resistant strains. The subpocket 1-specific inhibitors exhibit a generally higher activity than subpocket 2-specific inhibitors, and they also hold a strong selectivity between their cognate and noncognate subpockets. Dynamics and energetics analyses reveal that the SaDHQS active site prefers to interact with amphipathic and polar inhibitors by forming multiple hydrogen bonds and van der Waals packing at the complex interfaces of the two subpockets with their cognate inhibitors.
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Affiliation(s)
- Quanfeng Liu
- Department of Anesthesiology, Yidu Central Hospital Affiliated to Weifang Medical University, Qingzhou 262500, P. R. China
| | - Liping Li
- Department of Obstetrics, Yidu Central Hospital Affiliated to Weifang Medical University, Qingzhou 262500, P. R. China
| | - Fei Xu
- Department of Anesthesiology, Yidu Central Hospital Affiliated to Weifang Medical University, Qingzhou 262500, P. R. China
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