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Alotaibi BS, Hakami MA, Jawaid T, Alshammari N, Binsuwaidan R, Adnan M. Identification of potential Escherichia coli DNA gyrase B inhibitors targeting antibacterial therapy: an integrated docking and molecular dynamics simulation study. J Biomol Struct Dyn 2023:1-12. [PMID: 37608545 DOI: 10.1080/07391102.2023.2249117] [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: 05/16/2023] [Accepted: 08/10/2023] [Indexed: 08/24/2023]
Abstract
The alarming rise in the rate of antibiotic resistance is a matter of significant concern. DNA gyrase B (GyrB), a critical bacterial enzyme involved in DNA replication, transcription, and recombination, has emerged as a promising target for antibacterial agents. Inhibition of GyrB disrupts bacterial DNA replication, leading to cell death, making it an attractive candidate for antibiotic development. Although several classes of antibiotics targeting GyrB are currently in clinical use, the emergence of antibiotic resistance necessitates the exploration of novel inhibitors. In this study, we aimed to identify potential Escherichia coli GyrB inhibitors from a database of phytoconstituents sourced from Indian medicinal plants. Utilizing virtual screening, we performed a rigorous search to identify compounds with the most promising inhibitory properties against GyrB. Two compounds, namely Zizogenin and Cucurbitacin S, were identified based on their favorable drug likeliness and pharmacokinetic profiles. Employing advanced computational techniques, we analyzed the binding interactions of Zizogenin and Cucurbitacin S with the ATP-binding site of GyrB through molecular docking simulations. Both compounds exhibited robust binding interactions, evidenced by their high docking energy scores. To assess the stability of these interactions, we conducted extensive 100 ns molecular dynamics (MD) simulations, which confirmed the stability of Zizogenin and Cucurbitacin S when bound to GyrB. In conclusion, our study highlights Zizogenin and Cucurbitacin S as promising candidates for potential antibacterial agents targeting GyrB. Experimental validation of these compounds is warranted to further explore their efficacy and potential as novel antibiotics to combat antibiotic-resistant bacteria.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bader S Alotaibi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al-Quwayiyah, Shaqra University, Riyadh, Saudi Arabia
| | - Mohammed Ageeli Hakami
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al-Quwayiyah, Shaqra University, Riyadh, Saudi Arabia
| | - Talha Jawaid
- Department of Pharmacology, College of Medicine, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Nawaf Alshammari
- Department of Biology, College of Science, University of Ha'il, Hail, Saudi Arabia
| | - Reem Binsuwaidan
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Mohd Adnan
- Department of Biology, College of Science, University of Ha'il, Hail, Saudi Arabia
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2
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Roney M, Issahaku AR, Forid MS, Huq AKMM, Soliman MES, Mohd Aluwi MFF, Tajuddin SN. In silico evaluation of usnic acid derivatives to discover potential antibacterial drugs against DNA gyrase B and DNA topoisomerase IV. J Biomol Struct Dyn 2023; 41:14904-14913. [PMID: 36995164 DOI: 10.1080/07391102.2023.2193996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 02/18/2023] [Indexed: 03/31/2023]
Abstract
Due to the rising increase in infectious diseases brought on by bacteria and anti-bacterial drug resistance, antibacterial therapy has become difficult. The majority of first-line antibiotics are no longer effective against numerous germs, posing a new hazard to global human health in the 21st century. Through the drug-likeness screening, 184 usnic acid derivatives were selected from an in-house database of 340 usnic acid compounds. The pharmacokinetics (ADMET) prediction produced fifteen hit compounds, of which the lead molecule was subsequently obtained through a molecular docking investigation. The lead compounds, labelled compound-277 and compound-276, respectively, with the substantial binding affinity towards the enzymes were obtained through further docking simulation on the DNA gyrase and DNA topoisomerase proteins. Additionally, molecular dynamic (MD) simulation was performed for 300 ns on the lead compounds in order to confirm the stability of the docked complexes and the binding pose discovered during docking tests. Due to their intriguing pharmacological characteristics, these substances may be promising therapeutic candidate for anti-bacterial medication.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Miah Roney
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang Lebuhraya Tun Razak, Gambang, Kuantan, Pahang Darul Makmur, Malaysia
- Bio Aromatic Research Centre, Universiti Malaysia Pahang Lebuhraya Tun Razak, Gambang, Kuantan, Pahang Darul Makmur, Malaysia
| | - Abdul Rashid Issahaku
- West African Centre for Computational Analysis, Accra, Ghana
- Molecular Bio-computation and Drug Design Laboratory, Discipline of Pharmaceutical Sciences, University of KwaZulu-Natal, Westville Campus, Durban, South Africa
| | - Md Shaekh Forid
- Faculty of Chemical and Process Engineering Technology, Universiti Malaysia Pahang Lebuhraya Tun Razak, Gambang, Kuantan, Pahang Darul Makmur, Malaysia
| | - A K M Moyeenul Huq
- Bio Aromatic Research Centre, Universiti Malaysia Pahang Lebuhraya Tun Razak, Gambang, Kuantan, Pahang Darul Makmur, Malaysia
- Department of Pharmacy, School of Medicine, University of Asia Pacific, Dhaka, Bangladesh
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Laboratory, Discipline of Pharmaceutical Sciences, University of KwaZulu-Natal, Westville Campus, Durban, South Africa
| | - Mohd Fadhlizil Fasihi Mohd Aluwi
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang Lebuhraya Tun Razak, Gambang, Kuantan, Pahang Darul Makmur, Malaysia
- Bio Aromatic Research Centre, Universiti Malaysia Pahang Lebuhraya Tun Razak, Gambang, Kuantan, Pahang Darul Makmur, Malaysia
| | - Saiful Nizam Tajuddin
- Bio Aromatic Research Centre, Universiti Malaysia Pahang Lebuhraya Tun Razak, Gambang, Kuantan, Pahang Darul Makmur, Malaysia
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3
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Discovery of oxazoline-triazole based hybrid molecules as DNA gyrase inhibitors: A new class of potential Anti-tubercular agents. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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4
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Kumar S, Devi J, Dubey A, Kumar D, Jindal DK, Asija S, Sharma A. Co(II), Ni(II), Cu(II) and Zn(II) complexes of Schiff base ligands: synthesis, characterization, DFT, in vitro antimicrobial activity and molecular docking studies. RESEARCH ON CHEMICAL INTERMEDIATES 2022. [DOI: 10.1007/s11164-022-04941-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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5
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Salman M, Sharma P, Kumar M, Ethayathulla AS, Kaur P. Targeting novel sites in DNA gyrase for development of anti-microbials. Brief Funct Genomics 2022; 22:180-194. [PMID: 36064602 DOI: 10.1093/bfgp/elac029] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 07/28/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
Antimicrobial resistance in bacteria poses major challenges in selection of the therapeutic regime for managing the infectious disease. There is currently an upsurge in the appearance of multiple drug resistance in bacterial pathogens and a decline in the discovery of novel antibiotics. DNA gyrase is an attractive target used for antibiotic discovery due to its vital role in bacterial DNA replication and segregation in addition to its absence in mammalian organisms. Despite the presence of successful antibiotics targeting this enzyme, there is a need to bypass the resistance against this validated drug target. Hence, drug development in DNA gyrase is a highly active research area. In addition to the conventional binding sites for the novobiocin and fluoroquinolone antibiotics, several novel sites are being exploited for drug discovery. The binding sites for novel bacterial type II topoisomerase inhibitor (NBTI), simocyclinone, YacG, Thiophene and CcdB are structurally and biochemically validated active sites, which inhibit the supercoiling activity of topoisomerases. The novel chemical moieties with varied scaffolds have been identified to target DNA gyrase. Amongst them, the NBTI constitutes the most advanced DNA gyrase inhibitor which are in phase III trial of drug development. The present review aims to classify the novel binding sites other than the conventional novobiocin and quinolone binding pocket to bypass the resistance due to mutations in the DNA gyrase enzyme. These sites can be exploited for the identification of new scaffolds for the development of novel antibacterial compounds.
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Affiliation(s)
- Mohd Salman
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Priyanka Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Mukesh Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - A S Ethayathulla
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
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6
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Muhammed MT, Kuyucuklu G, Kaynak-Onurdag F, Aki-Yalcin E. Synthesis, Antimicrobial Activity, and Molecular Modeling Studies of
Some Benzoxazole Derivatives. LETT DRUG DES DISCOV 2022. [DOI: 10.2174/1570180819666220408133643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
The need to develop novel antimicrobial agents is apparent as infectious diseases
are increasing and resistance is rapidly developing against the drugs used in the treatment.
Objective:
This study aimed at the synthesis, antimicrobial susceptibility testing, and computational elucidation
of the mechanism of action of benzoxazole derivatives. It also aimed to compare the results obtained
in this study with the previous studies by our group. This would pave the way for designing novel
molecules with better antimicrobial activity. The other goal was pharmacophore analysis and in silico
ADMET analysis of them.
Methods:
In this study, synthesis, antimicrobial susceptibility testing, molecular docking, pharmacophore
analysis, and ADMET prediction were carried out.
Results:
The antimicrobial activity studies demonstrated that the synthesized compounds were active
against standard strains and clinical isolates at high concentrations. Then, the antimicrobial testing results
were compared to similar benzoxazoles tested by our group previously. Benzoxazole derivatives without
a methylene bridge between oxazole and phenyl ring were found to be more active than those with the
methylene bridge. This was also confirmed by molecular modeling undertaken in this study. The computational
results indicated that the antibacterial activity could be achieved by DNA gyrase inhibition.
Pharmacophore analysis showed that hydrogen bond acceptor (HBA), hydrogen bond donor (HBD), and
hydrophobicity features would contribute to the inhibition. In addition, in silico ADMET property investigation
of the compounds exhibited that they had the desired pharmacokinetics.
Conclusion:
Although antibacterial activity by inhibiting DNA gyrase is selective, the synthesized compounds
were active at much higher concentrations than the standards. Therefore, in prospective antimicrobial
studies, it is better to focus on benzoxazole derivatives without the methylene bridge. Since the
compounds had suitable in silico ADMET properties, screening them against the other pharmacologic
activities should be carried out. It is recommended to support the molecular modeling results with in vitro
or in vivo studies.
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Affiliation(s)
- Muhammed Tilahun Muhammed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Suleyman Demirel University, Isparta, Turkey
- Department of Basic Biotechnology, Institute of Biotechnology, Ankara University, Ankara, Turkey
| | - Gulcan Kuyucuklu
- Department of Medical Microbiology, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Fatma Kaynak-Onurdag
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Trakya University, Edirne, Turkey
| | - Esin Aki-Yalcin
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ankara University, Ankara, Turkey
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7
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Egil AC, Ozdemir B, Gunduz SK, Altıkatoglu-Yapaoz M, Budama-Kilinc Y, Mostafavi E. Chitosan/calcium nanoparticles as advanced antimicrobial coating for paper documents. Int J Biol Macromol 2022; 215:521-530. [PMID: 35764166 DOI: 10.1016/j.ijbiomac.2022.06.142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 06/04/2022] [Accepted: 06/20/2022] [Indexed: 12/17/2022]
Abstract
Preservation of paper-based historical artifacts against deterioration due to the presence of bacteria and fungi colonies has been one of the major issues for the importance of protecting the cultural heritage of humankind. Advances in nanotechnology have enabled the implementation of nanomaterials for this purpose. In this work, calcium/chitosan nanoparticles (Ca/CS NPs) were prepared and well-characterized to investigate their potential as a novel approach for preserving paper-based documents. Following the fundamental characterizations, it was found that Ca/CS NPs are spherical nanoparticles with ~65 nm average size and homogenous dispersion (PdI: 0.2). Besides, minimum inhibition concentration results revealed that Ca/CS NPs show a superior antimicrobial effect against specific bacteria and fungi strains commonly found on paper documents compared to the effect of bare chitosan nanoparticles (CS NPs). After the deposition of Ca/CS NPs onto the paper the pH level was increased and stabilized, and only a limited amount of microbial colony formation was observed for up to 20 days. Moreover, molecular docking analysis provided a better insight into the antibacterial and antifungal activities of these nanoparticles. The antimicrobial activity of CS NPs and Ca/CS NPs was investigated through their interactions with E. coli DNA gyrase B and C. albicans dihydrofolate reductase. The binding modes and all possible interactions of active sites were confirmed by in silico molecular docking method. Collectively, our findings revealed that the formulated Ca/CS NPs are promising candidates for preserving paper documents.
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Affiliation(s)
- Abdurrahim Can Egil
- Sabancı University, Faculty of Engineering and Natural Sciences, Department of Materials Science and Nanoengineering, 34956 İstanbul, Turkey; Piccolo Nanotechnology and Engineering Limited Company, Yildiz Technopark, 34220 Istanbul, Turkey
| | - Burak Ozdemir
- Acıbadem Mehmet Ali Aydınlar University, Faculty of Engineering, Department of Medical Engineering, Istanbul, Turkey
| | - Serda Kecel Gunduz
- Istanbul University, Faculty of Science, Physics Department, 34134 Istanbul, Turkey
| | - Melda Altıkatoglu-Yapaoz
- Yildiz Technical University, Faculty of Art and Sciences, Department of Chemistry, Istanbul 34220, Turkey
| | - Yasemin Budama-Kilinc
- Yildiz Technical University, Faculty of Chemical and Metallurgical Engineering, Department of Bioengineering, 34220 İstanbul, Turkey
| | - Ebrahim Mostafavi
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cardiovascular Institute, Stanford University School of Medicine, CA 94305, USA.
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8
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Foudah AI, Alqarni MH, Alam A, Salkini MA, Ross SA, Yusufoglu HS. Phytochemical Screening, In Vitro and In Silico Studies of Volatile Compounds from Petroselinum crispum (Mill) Leaves Grown in Saudi Arabia. Molecules 2022; 27:molecules27030934. [PMID: 35164196 PMCID: PMC8840193 DOI: 10.3390/molecules27030934] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/21/2022] [Accepted: 01/27/2022] [Indexed: 11/16/2022] Open
Abstract
The herbal plant Petroselinum crispum (P. crispum) (Mill) is commonly available around the world. In this study, the leaves of the herbal plant P. crispum were collected from the central region of Al-Kharj, Saudi Arabia, to explore their in vitro pharmacological activity. Essential oil from the leaves of P. crispum was isolated using the hydrodistillation method. The composition of P. crispum essential oil (PCEO) was determined using Gas chromatography-mass spectrometry (GC-MS). A total of 67 components were identified, representing approximately 96.02% of the total volatile composition. Myristicin was identified as the principal constituent (41.45%). The in vitro biological activity was assessed to evaluate the antioxidant, antimicrobial, and anti-inflammatory potential of PCEO. PCEO showed the highest antimicrobial activity against Candida albicans and Staphylococcus aureus among all the evaluated microbial species. In vitro anti-inflammatory evaluation using albumin and trypsin assays showed the excellent anti-inflammatory potential of PCEO compared to the standard drugs. An in silico study of the primary PCEO compound was conducted using online tools such as PASS, Swiss ADME, and Molecular docking. In silico PASS prediction results supported our in vitro findings. Swiss ADME revealed the drug likeness and safety properties of the major metabolites present in PCEO. Molecular docking results were obtained by studying the interaction of Myristicin with an antifungal (PDB: 1IYL and 3LD6), antibacterial (PDB: 1AJ6 and 1JIJ), antioxidant (PDB: 3NM8 and 1HD2), and anti-inflammatory (3N8Y and 3LN1) receptors supported the in vitro results. Therefore, PCEO or Myristicin might be valuable for developing anti-inflammatory and antimicrobial drugs.
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Affiliation(s)
- Ahmed I. Foudah
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al Kharj 11942, Saudi Arabia; (M.H.A.); (A.A.); (M.A.S.)
- Correspondence:
| | - Mohammad H. Alqarni
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al Kharj 11942, Saudi Arabia; (M.H.A.); (A.A.); (M.A.S.)
| | - Aftab Alam
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al Kharj 11942, Saudi Arabia; (M.H.A.); (A.A.); (M.A.S.)
| | - Mohammad Ayman Salkini
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al Kharj 11942, Saudi Arabia; (M.H.A.); (A.A.); (M.A.S.)
| | - Samir A. Ross
- National Center for Natural Products Research, School of Pharmacy, The University of Mississippi, University, MS 38677, USA;
- Department of Biomolecular Sciences, School of Pharmacy, The University of Mississippi, University, MS 38677, USA
| | - Hasan S. Yusufoglu
- Department of Pharmacognosy & Pharmaceutical Chemistry, College of Dentistry & Pharmacy, Buraydah Private College, Buraydah 81418, Saudi Arabia;
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9
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Elseginy SA, Anwar MM. Pharmacophore-Based Virtual Screening and Molecular Dynamics Simulation for Identification of a Novel DNA Gyrase B Inhibitor with Benzoxazine Acetamide Scaffold. ACS OMEGA 2022; 7:1150-1164. [PMID: 35036778 PMCID: PMC8756603 DOI: 10.1021/acsomega.1c05732] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/14/2021] [Indexed: 05/10/2023]
Abstract
DNA gyrase B is one of the enzyme targets for antimicrobial drug development, and its absence in mammals makes it a suitable target for the creation of safe antibacterial drugs. We identified six novel hits as DNA gyrase B inhibitors in the present study by employing 3D-pharmacophore structure-based virtual screening. The lead compounds complied with drug-likeness rules and lacked toxicity. Compound 4 (ZINC32858011) showed the highest inhibitory activity with an IC50 value of 6.3 ± 0.1 μM against the DNA gyrase enzyme. In contrast, the positive controls ciprofloxacin and novobiocin used in enzyme inhibition assay had IC50 values of 14.4 ± 0.2 and 12.4 ± 0.2 μM, respectively. The molecular docking of the six hits demonstrated that compounds 1, 2, 4, and 6 had suitable fitting modes inside the binding pocket. Molecular dynamics simulations were carried out for the six hits and the rmsd, rmsf, radius of gyration, and solvent accessible surface area parameters obtained from 100 ns molecular dynamics simulations for the six compounds complexed with a DNA gyrase B protein indicated that compound 4 (ZINC32858011) formed the most stable complex with DNA gyrase B. The binding free energy calculation with the MM-PBSA method suggested that the van der Waals interaction, followed by electrostatic force, played a significant role in the binding. Per-residue free binding energy decomposition showed that Ile78 contributed the most for the binding energy followed by Asn46, Asp49, Glu50, Asp73, Ile78, Pro79, Ala86, Ile90, Val120, Thr165, and Val167.
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Affiliation(s)
- Samia A. Elseginy
- Green
Chemistry Department, Chemical Industries Research Division, National Research Centre, Dokki, Cairo 12622, Egypt
- . Phone: +20(1150882009)
| | - Manal M. Anwar
- Therapeutical
Chemistry Department, National Research
Centre, Dokki, Cairo 12622, Egypt
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10
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Singh M, Anthal S, Chandrasekaran R, Murugavel S, Sankpal SS, Deshmukh MB, Kant R. Crystallographic Structure and in Silico Molecular Docking Analysis of 2-Cyclohexylidene-Hydrazine-Carbothiomide. CRYSTALLOGR REP+ 2021. [DOI: 10.1134/s1063774521070178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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11
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Ninh The S, Le Tuan A, Dinh Thi Thu T, Nguyen Dinh L, Tran Thi T, Pham-The H. Essential oils of Uvaria boniana - chemical composition, in vitro bioactivity, docking, and in silico ADMET profiling of selective major compounds. Z NATURFORSCH C 2021; 77:207-218. [PMID: 34761648 DOI: 10.1515/znc-2021-0111] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 10/16/2021] [Indexed: 02/07/2023]
Abstract
Phytochemical investigation applying GC (gas chromatography)-MS (mass spectrometry)/GC-FID (flame ionization detection) on the hydro-distilled essential oils of the Vietnamese medicinal plant Uvaria boniana leaf and twig lead to the detection of 35 constituents (97.36%) in the leaf oil and 52 constituents (98.75%) in the twig oil. Monoterpenes, monoterpenoids, sesquiterpenes, and sesquiterpenoids were characteristic of U. boniana essential oils. The leaf oil was represented by major components (E)-caryophyllene (16.90%), bicyclogermacrene (15.95%), α-humulene (14.96%), and linalool (12.40%), whereas four compounds α-cadinol (16.16%), epi-α-muurolol (10.19%), α-pinene (11.01%), and β-pinene (8.08%) were the main ones in the twig oil. As compared with the leaf oil, the twig oil was better in antimicrobial activity. With the same MIC value of 40 mg/mL, the twig oil successfully controlled the growth of Gram (+) bacterium Bacillus subtilis, Gram (-) bacterium Escherichia coli, fungus Aspergillus niger, and yeast Saccharomyces cerevisiae. In addition, both two oil samples have induced antiinflammatory activity with the IC50 values of 223.7-240.6 mg/mL in NO productive inhibition when BV2 cells had been stimulated by LPS. Docking simulations of four major compounds of U. boniana twig oil on eight relevant antibacterial targets revealed that epi-α-muurolol and α-cadinol are moderate inhibitors of E. coli DNA gyrase subunit B, penicillin binding protein 2X and penicillin binding protein 3 of Pseudomonas aeruginosa with similar free binding energies of -30.1, -29.3, and -29.3 kJ/mol, respectively. Furthermore, in silico ADMET studies indicated that all four docked compounds have acceptable oral absorption, low metabolism, and appropriated toxicological profile to be considered further as drug candidates.
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Affiliation(s)
- Son Ninh The
- Institute of Chemistry, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Caugiay, Hanoi, Vietnam
| | - Anh Le Tuan
- Mien Trung Institute for Scientific Research, VAST, Hanoi, Vietnam
| | | | | | - Tuyen Tran Thi
- Institute of Natural Products Chemistry, VAST, Hanoi, Vietnam.,Graduate University of Science and Technology, VAST, Hanoi, Vietnam
| | - Hai Pham-The
- Hanoi University of Pharmacy, 13-15 Le Thanh Tong, Hoan Kiem, Hanoi, Vietnam
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12
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El-Saghier AM, El-Naggar M, Hussein AHM, El-Adasy ABA, Olish M, Abdelmonsef AH. Eco-Friendly Synthesis, Biological Evaluation, and In Silico Molecular Docking Approach of Some New Quinoline Derivatives as Potential Antioxidant and Antibacterial Agents. Front Chem 2021; 9:679967. [PMID: 34178944 PMCID: PMC8222571 DOI: 10.3389/fchem.2021.679967] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/14/2021] [Indexed: 12/12/2022] Open
Abstract
A new series of quinoline derivatives 5–12 were efficiently synthesized via one-pot multicomponent reaction (MCR) of resorcinol, aromatic aldehydes, β-ketoesters, and aliphatic/aromatic amines under solvent-free conditions. All products were obtained in excellent yields, pure at low-cost processing, and short time. The structures of all compounds were characterized by means of spectral and elemental analyses. In addition, all the synthesized compounds 5–12 were in vitro screened for their antioxidant and antibacterial activity. Moreover, in silico molecular docking studies of the new quinoline derivatives with the target enzymes, human NAD (P)H dehydrogenase (quinone 1) and DNA gyrase, were achieved to endorse their binding affinities and to understand ligand–enzyme possible intermolecular interactions. Compound 9 displayed promising antioxidant and antibacterial activity, as well as it was found to have the highest negative binding energy of -9.1 and -9.3 kcal/mol for human NAD (P)H dehydrogenase (quinone 1) and DNA gyrase, respectively. Further, it complied with the Lipinski’s rule of five, Veber, and Ghose. Therefore, the quinoline analogue 9 could be promising chemical scaffold for the development of future drug candidates as antioxidant and antibacterial agents.
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Affiliation(s)
- Ahmed M El-Saghier
- Chemistry Department, Faculty of Science, Sohag University, Sohag, Egypt
| | - Mohamed El-Naggar
- Chemistry Department, Faculty of Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | | | - Abu-Bakr A El-Adasy
- Chemistry Department, Faculty of Science, Al-Azhar University, Assiut, Egypt
| | - M Olish
- Chemistry Department, Faculty of Science, Al-Azhar University, Assiut, Egypt
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13
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Novel Amino Acid Derivatives of Quinolines as Potential Antibacterial and Fluorophore Agents. Sci Pharm 2020. [DOI: 10.3390/scipharm88040057] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
A new series of amino acid derivatives of quinolines was synthesized through the hydrolysis of amino acid methyl esters of quinoline carboxamides with alkali hydroxide. The compounds were purified on silica gel by column chromatography and further characterized by TLC, NMR and ESI-TOF mass spectrometry. All compounds were screened for in vitro antimicrobial activity against different bacterial strains using the microdilution method. Most of the synthesized amino acid-quinolines show more potent or equipotent inhibitory action against the tested bacteria than their correspond esters. In addition, many of them exhibit fluorescent properties and could possibly be utilized as fluorophores. Molecular docking and simulation studies of the compounds at putative bacterial target enzymes suggest that the antimicrobial potency of these synthesized analogues could be due to enzyme inhibition via their favorable binding at the fluoroquinolone binding site at the GyrA subunit of DNA gyrase and/or the ParC subunit of topoisomerase-IV.
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14
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Mohi El-Deen EM, Abd El-Meguid EA, Karam EA, Nossier ES, Ahmed MF. Synthesis and Biological Evaluation of New Pyridothienopyrimidine Derivatives as Antibacterial Agents and Escherichia coli Topoisomerase II Inhibitors. Antibiotics (Basel) 2020; 9:antibiotics9100695. [PMID: 33066400 PMCID: PMC7602199 DOI: 10.3390/antibiotics9100695] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/30/2020] [Accepted: 10/07/2020] [Indexed: 11/16/2022] Open
Abstract
The growing resistance of bacteria to many antibiotics that have been in use for several decades has generated the need to discover new antibacterial agents with structural features qualifying them to overcome the resistance mechanisms. Thus, novel pyridothienopyrimidine derivatives (2a,b-a,b) were synthesized by a series of various reactions, starting with 3-aminothieno[2,3-b]pyridine-2-carboxamides (1a,b). Condensation of compounds 1a,b with cyclohexanone gave 1'H-spiro[cyclohexane-1,2'-pyrido[3',2':4,5]thieno[3,2-d]pyrimidin]-4'(3'H)-ones (2a,b), which in turn were utilized to afford the target 4-substituted derivatives (3a,b-8a,b). In vitro antibacterial activity evaluations of all the new compounds (2a,b-8a,b) were performed against six strains of Gram-negative and Gram-positive bacteria. The target compounds showed significant antibacterial activity, especially against Gram-negative strains. Moreover, the compounds (2a,b; 3a,b; 4a,b; and 5a,b) that exhibited potent activity against Escherichia coli were selected to screen their inhibitory activity against Escherichia coli topoisomerase II (DNA gyrase and topoisomerase IV) enzymes. Compounds 4a and 4b showed potent dual inhibition of the two enzymes with IC50 values of 3.44 µΜ and 5.77 µΜ against DNA gyrase and 14.46 µΜ and 14.89 µΜ against topoisomerase IV, respectively. In addition, docking studies were carried out to give insight into the binding mode of the tested compounds within the E. coli DNA gyrase B active site compared with novobiocin.
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Affiliation(s)
- Eman M. Mohi El-Deen
- Department of Therapeutic Chemistry, National Research Centre, Dokki, Cairo 12622, Egypt
- Correspondence: ; Tel.: +20-0106-385-3338
| | - Eman A. Abd El-Meguid
- Department of Chemistry of Natural and Microbial Products, National Research Centre, Dokki, Cairo 12622, Egypt;
| | - Eman A. Karam
- Microbial Chemistry Department, National Research Centre, Dokki, Cairo 12622, Egypt;
| | - Eman S. Nossier
- Department of Pharmaceutical Medicinal Chemistry, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo 11754, Egypt;
| | - Marwa F. Ahmed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Taif University, Taif 21974, Saudi Arabia;
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Helwan University, Cairo 11795, Egypt
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15
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Henderson SR, Stevenson CEM, Malone B, Zholnerovych Y, Mitchenall LA, Pichowicz M, McGarry DH, Cooper IR, Charrier C, Salisbury AM, Lawson DM, Maxwell A. Structural and mechanistic analysis of ATPase inhibitors targeting mycobacterial DNA gyrase. J Antimicrob Chemother 2020; 75:2835-2842. [PMID: 32728686 PMCID: PMC7556816 DOI: 10.1093/jac/dkaa286] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 05/28/2020] [Accepted: 05/30/2020] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVES To evaluate the efficacy of two novel compounds against mycobacteria and determine the molecular basis of their action on DNA gyrase using structural and mechanistic approaches. METHODS Redx03863 and Redx04739 were tested in antibacterial assays, and also against their target, DNA gyrase, using DNA supercoiling and ATPase assays. X-ray crystallography was used to determine the structure of the gyrase B protein ATPase sub-domain from Mycobacterium smegmatis complexed with the aminocoumarin drug novobiocin, and structures of the same domain from Mycobacterium thermoresistibile complexed with novobiocin, and also with Redx03863. RESULTS Both compounds, Redx03863 and Redx04739, were active against selected Gram-positive and Gram-negative species, with Redx03863 being the more potent, and Redx04739 showing selectivity against M. smegmatis. Both compounds were potent inhibitors of the supercoiling and ATPase reactions of DNA gyrase, but did not appreciably affect the ATP-independent relaxation reaction. The structure of Redx03863 bound to the gyrase B protein ATPase sub-domain from M. thermoresistibile shows that it binds at a site adjacent to the ATP- and novobiocin-binding sites. We found that most of the mutations that we made in the Redx03863-binding pocket, based on the structure, rendered gyrase inactive. CONCLUSIONS Redx03863 and Redx04739 inhibit gyrase by preventing the binding of ATP. The fact that the Redx03863-binding pocket is distinct from that of novobiocin, coupled with the lack of activity of resistant mutants, suggests that such compounds could have potential to be further exploited as antibiotics.
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Affiliation(s)
- Sara R Henderson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
- Norwich Medical School, University of East Anglia, Norwich NR4 7UQ, UK
| | - Clare E M Stevenson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Brandon Malone
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Yelyzaveta Zholnerovych
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Lesley A Mitchenall
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Mark Pichowicz
- Redx Pharma PLC, Mereside, Alderley Park, Alderley Edge SK10 4TG, UK
- Sygnature Discovery, The Discovery Building, Biocity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - David H McGarry
- Redx Pharma PLC, Mereside, Alderley Park, Alderley Edge SK10 4TG, UK
- Globachem Discovery Ltd, Mereside, Alderley Park SK10 4TG, UK
| | - Ian R Cooper
- Redx Pharma PLC, Mereside, Alderley Park, Alderley Edge SK10 4TG, UK
- AMR Centre Ltd, Mereside, Alderley Park SK10 4TG, UK
| | - Cedric Charrier
- Redx Pharma PLC, Mereside, Alderley Park, Alderley Edge SK10 4TG, UK
- IHMA Europe Sàrl, Rte. de I’lle-au-Bois 1A, 1870 Monthey/VS, Switzerland
| | - Anne-Marie Salisbury
- Redx Pharma PLC, Mereside, Alderley Park, Alderley Edge SK10 4TG, UK
- 5D Health Protection Group Ltd, William Henry Duncan Building, West Derby Street, Liverpool L7 8TX, UK
| | - David M Lawson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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16
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Cordeiro L, Diniz-Neto H, Figueiredo P, Souza H, Sousa A, Andrade-Júnior F, Melo T, Ferreira E, Oliveira R, Athayde-Filho P, Barbosa-Filho J, Oliveira-Filho A, Lima E. Potential of 2-Chloro- N-(4-fluoro-3-nitrophenyl)acetamide Against Klebsiella pneumoniae and In Vitro Toxicity Analysis. Molecules 2020; 25:molecules25173959. [PMID: 32877986 PMCID: PMC7504751 DOI: 10.3390/molecules25173959] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 07/18/2020] [Accepted: 07/21/2020] [Indexed: 11/16/2022] Open
Abstract
Klebsiella pneumoniae causes a wide range of community and nosocomial infections. The high capacity of this pathogen to acquire resistance drugs makes it necessary to develop therapeutic alternatives, discovering new antibacterial molecules. Acetamides are molecules that have several biological activities. However, there are no reports on the activity of 2-chloro-N-(4-fluoro-3-nitrophenyl)acetamide. Based on this, this study aimed to investigate the in vitro antibacterial activity of this molecule on K. pneumoniae, evaluating whether the presence of the chloro atom improves this effect. Then, analyzing its antibacterial action more thoroughly, as well as its cytotoxic and pharmacokinetic profile, in order to contribute to future studies for the viability of a new antibacterial drug. It was shown that the substance has good potential against K. pneumoniae and the chloro atom is responsible for improving this activity, stabilizing the molecule in the target enzyme at the site. The substance possibly acts on penicillin-binding protein, promoting cell lysis. The analysis of cytotoxicity and mutagenicity shows favorable results for future in vivo toxicological tests to be carried out, with the aim of investigating the potential of this molecule. In addition, the substance showed an excellent pharmacokinetic profile, indicating good parameters for oral use.
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Affiliation(s)
- Laísa Cordeiro
- Department of Pharmaceutical Science, Health Sciences Center, Federal University of Paraíba, 58033-455 João Pessoa, Paraíba, Brazil; (H.D.-N.); (P.F.); (A.S.); (F.A.-J.); (T.M.); (E.F.); (J.B.-F.); (E.L.)
- Correspondence: ; Tel.: +55-83-3216-7347
| | - Hermes Diniz-Neto
- Department of Pharmaceutical Science, Health Sciences Center, Federal University of Paraíba, 58033-455 João Pessoa, Paraíba, Brazil; (H.D.-N.); (P.F.); (A.S.); (F.A.-J.); (T.M.); (E.F.); (J.B.-F.); (E.L.)
| | - Pedro Figueiredo
- Department of Pharmaceutical Science, Health Sciences Center, Federal University of Paraíba, 58033-455 João Pessoa, Paraíba, Brazil; (H.D.-N.); (P.F.); (A.S.); (F.A.-J.); (T.M.); (E.F.); (J.B.-F.); (E.L.)
| | - Helivaldo Souza
- Chemistry Department, Exact and Natural Sciences Center, Federal University of Paraíba, 58033-455 João Pessoa, Brazil; (H.S.); (R.O.); (P.A.-F.)
| | - Aleson Sousa
- Department of Pharmaceutical Science, Health Sciences Center, Federal University of Paraíba, 58033-455 João Pessoa, Paraíba, Brazil; (H.D.-N.); (P.F.); (A.S.); (F.A.-J.); (T.M.); (E.F.); (J.B.-F.); (E.L.)
| | - Francisco Andrade-Júnior
- Department of Pharmaceutical Science, Health Sciences Center, Federal University of Paraíba, 58033-455 João Pessoa, Paraíba, Brazil; (H.D.-N.); (P.F.); (A.S.); (F.A.-J.); (T.M.); (E.F.); (J.B.-F.); (E.L.)
| | - Thamara Melo
- Department of Pharmaceutical Science, Health Sciences Center, Federal University of Paraíba, 58033-455 João Pessoa, Paraíba, Brazil; (H.D.-N.); (P.F.); (A.S.); (F.A.-J.); (T.M.); (E.F.); (J.B.-F.); (E.L.)
| | - Elba Ferreira
- Department of Pharmaceutical Science, Health Sciences Center, Federal University of Paraíba, 58033-455 João Pessoa, Paraíba, Brazil; (H.D.-N.); (P.F.); (A.S.); (F.A.-J.); (T.M.); (E.F.); (J.B.-F.); (E.L.)
| | - Rafael Oliveira
- Chemistry Department, Exact and Natural Sciences Center, Federal University of Paraíba, 58033-455 João Pessoa, Brazil; (H.S.); (R.O.); (P.A.-F.)
| | - Petrônio Athayde-Filho
- Chemistry Department, Exact and Natural Sciences Center, Federal University of Paraíba, 58033-455 João Pessoa, Brazil; (H.S.); (R.O.); (P.A.-F.)
| | - José Barbosa-Filho
- Department of Pharmaceutical Science, Health Sciences Center, Federal University of Paraíba, 58033-455 João Pessoa, Paraíba, Brazil; (H.D.-N.); (P.F.); (A.S.); (F.A.-J.); (T.M.); (E.F.); (J.B.-F.); (E.L.)
| | - Abrahão Oliveira-Filho
- Rural Health and Technology Center, Federal University of Campina Grande, 58708-110 Patos, Brazil;
| | - Edeltrudes Lima
- Department of Pharmaceutical Science, Health Sciences Center, Federal University of Paraíba, 58033-455 João Pessoa, Paraíba, Brazil; (H.D.-N.); (P.F.); (A.S.); (F.A.-J.); (T.M.); (E.F.); (J.B.-F.); (E.L.)
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17
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Recent advances in DNA gyrase-targeted antimicrobial agents. Eur J Med Chem 2020; 199:112326. [DOI: 10.1016/j.ejmech.2020.112326] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 04/07/2020] [Accepted: 04/08/2020] [Indexed: 12/16/2022]
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18
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Structure-Based Drug Design for Tuberculosis: Challenges Still Ahead. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10124248] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Structure-based and computer-aided drug design approaches are commonly considered to have been successful in the fields of cancer and antiviral drug discovery but not as much for antibacterial drug development. The search for novel anti-tuberculosis agents is indeed an emblematic example of this trend. Although huge efforts, by consortiums and groups worldwide, dramatically increased the structural coverage of the Mycobacterium tuberculosis proteome, the vast majority of candidate drugs included in clinical trials during the last decade were issued from phenotypic screenings on whole mycobacterial cells. We developed here three selected case studies, i.e., the serine/threonine (Ser/Thr) kinases—protein kinase (Pkn) B and PknG, considered as very promising targets for a long time, and the DNA gyrase of M. tuberculosis, a well-known, pharmacologically validated target. We illustrated some of the challenges that rational, target-based drug discovery programs in tuberculosis (TB) still have to face, and, finally, discussed the perspectives opened by the recent, methodological developments in structural biology and integrative techniques.
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19
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Ushiyama F, Amada H, Takeuchi T, Tanaka-Yamamoto N, Kanazawa H, Nakano K, Mima M, Masuko A, Takata I, Hitaka K, Iwamoto K, Sugiyama H, Ohtake N. Lead Identification of 8-(Methylamino)-2-oxo-1,2-dihydroquinoline Derivatives as DNA Gyrase Inhibitors: Hit-to-Lead Generation Involving Thermodynamic Evaluation. ACS OMEGA 2020; 5:10145-10159. [PMID: 32391502 PMCID: PMC7203957 DOI: 10.1021/acsomega.0c00865] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/09/2020] [Indexed: 05/26/2023]
Abstract
DNA gyrase and topoisomerase IV are well-validated pharmacological targets, and quinolone antibacterial drugs are marketed as their representative inhibitors. However, in recent years, resistance to these existing drugs has become a problem, and new chemical classes of antibiotics that can combat resistant strains of bacteria are strongly needed. In this study, we applied our hit-to-lead (H2L) chemistry for the identification of a new chemical class of GyrB/ParE inhibitors by efficient use of thermodynamic parameters. Investigation of the core fragments obtained by fragmentation of high-throughput screening hit compounds and subsequent expansion of the hit fragment was performed using isothermal titration calorimetry (ITC). The 8-(methylamino)-2-oxo-1,2-dihydroquinoline derivative 13e showed potent activity against Escherichia coli DNA gyrase with an IC50 value of 0.0017 μM. In this study, we demonstrated the use of ITC for primary fragment screening, followed by structural optimization to obtain lead compounds, which advanced into further optimization for creating novel antibacterial agents.
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Affiliation(s)
- Fumihito Ushiyama
- Chemistry
Laboratories, Taisho Pharmaceutical Company
Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama 331-9530, Japan
| | - Hideaki Amada
- Chemistry
Laboratories, Taisho Pharmaceutical Company
Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama 331-9530, Japan
| | - Tomoki Takeuchi
- Chemistry
Laboratories, Taisho Pharmaceutical Company
Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama 331-9530, Japan
| | - Nozomi Tanaka-Yamamoto
- Chemistry
Laboratories, Taisho Pharmaceutical Company
Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama 331-9530, Japan
| | - Harumi Kanazawa
- Chemistry
Laboratories, Taisho Pharmaceutical Company
Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama 331-9530, Japan
| | - Koichiro Nakano
- Pharmacology
Laboratories, Taisho Pharmaceutical Company
Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama 331-9530, Japan
| | - Masashi Mima
- Pharmacology
Laboratories, Taisho Pharmaceutical Company
Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama 331-9530, Japan
| | - Aiko Masuko
- Pharmacology
Laboratories, Taisho Pharmaceutical Company
Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama 331-9530, Japan
| | - Iichiro Takata
- Pharmacology
Laboratories, Taisho Pharmaceutical Company
Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama 331-9530, Japan
| | - Kosuke Hitaka
- Pharmacology
Laboratories, Taisho Pharmaceutical Company
Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama 331-9530, Japan
| | - Kunihiko Iwamoto
- Pharmacology
Laboratories, Taisho Pharmaceutical Company
Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama 331-9530, Japan
| | - Hiroyuki Sugiyama
- Pharmacology
Laboratories, Taisho Pharmaceutical Company
Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama 331-9530, Japan
| | - Norikazu Ohtake
- Chemistry
Laboratories, Taisho Pharmaceutical Company
Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama 331-9530, Japan
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20
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Synthesis, Docking Studies, and In Vitro Evaluation of Some Novel Thienopyridines and Fused Thienopyridine-Quinolines as Antibacterial Agents and DNA Gyrase Inhibitors. Molecules 2019; 24:molecules24203650. [PMID: 31658631 PMCID: PMC6832920 DOI: 10.3390/molecules24203650] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 10/03/2019] [Accepted: 10/06/2019] [Indexed: 01/05/2023] Open
Abstract
A series of novel thienopyridines and pyridothienoquinolines (3a,b–14) was synthesized, starting with 2-thioxo-1,2-dihydropyridine-3-carbonitriles 1a and 1b. All compounds were evaluated for their in vitro antimicrobial activity against six bacterial strains. Compounds 3a,b, 4a, 5b, 6a,b, 7a, 9b, 12b, and 14 showed significant growth inhibition activity against both Gram-positive and Gram-negative bacteria compared with the reference drug. The most active compounds (4a, 7a, 9b, and 12b) against Staphylococcus aureus were also tested for their in vitro inhibitory action on methicillin-resistant Staphylococcus aureus (MRSA). The tested compounds showed promising inhibition activity, with the performance of 12b being equal to gentamicin and that of 7a exceeding it. Moreover, the most promising compounds were also screened for their Escherichia coli DNA gyrase inhibitory activity, compared with novobiocin as a reference DNA gyrase inhibitor. The results revealed that compounds (3a, 3b, 4a, 9b, and 12b) had the highest inhibitory capacity, with IC50 values of 2.26–5.87 µM (that of novobiocin is equal to 4.17 µM). Docking studies were performed to identify the mode of binding of the tested compounds to the active site of E. coli DNA gyrase B.
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21
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Darby JF, Hopkins AP, Shimizu S, Roberts SM, Brannigan JA, Turkenburg JP, Thomas GH, Hubbard RE, Fischer M. Water Networks Can Determine the Affinity of Ligand Binding to Proteins. J Am Chem Soc 2019; 141:15818-15826. [DOI: 10.1021/jacs.9b06275] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
| | - Adam P. Hopkins
- Demuris Ltd., The Biosphere, Draymans Way, Newcastle Helix, Newcastle upon Tyne NE4 5BX, United Kingdom
| | | | | | | | | | | | - Roderick E. Hubbard
- Vernalis (R&D) Ltd., Granta Park, Abington, Cambridge CB21 6GB, United Kingdom
| | - Marcus Fischer
- Department of Chemical Biology & Therapeutics, and Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
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22
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Lu Q, Qi LW, Liu J. Improving protein–ligand binding prediction by considering the bridging water molecules in Autodock. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2019. [DOI: 10.1142/s0219633619500275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Water plays a significant role in determining the protein–ligand binding modes, especially when water molecules are involved in mediating protein–ligand interactions, and these important water molecules are receiving more and more attention in recent years. Considering the effects of water molecules has gradually become a routine process for accurate description of the protein–ligand interactions. As a free docking program, Autodock has been most widely used in predicting the protein–ligand binding modes. However, whether the inclusion of water molecules in Autodock would improve its docking performance has not been systematically investigated. Here, we incorporate important bridging water molecules into Autodock program, and systematically investigate the effectiveness of these water molecules in protein–ligand docking. This approach was evaluated using 18 structurally diverse protein–ligand complexes, in which several water molecules bridge the protein–ligand interactions. Different treatment of water molecules were tested by using the fixed and rotatable water molecules, and a considerable improvement in successful docking simulations was found when including these water molecules. This study illustrates the necessity of inclusion of water molecules in Autodock docking, and emphasizes the importance of a proper treatment of water molecules in protein–ligand binding predictions.
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Affiliation(s)
- Qiangna Lu
- State Key Laboratory of Natural Medicines, Department of Chinese Medicine, Department of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Lian-Wen Qi
- State Key Laboratory of Natural Medicines, Department of Chinese Medicine, Department of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Jinfeng Liu
- State Key Laboratory of Natural Medicines, Department of Chinese Medicine, Department of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
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23
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Yi L, Lü X. New Strategy on Antimicrobial-resistance: Inhibitors of DNA Replication Enzymes. Curr Med Chem 2019; 26:1761-1787. [PMID: 29110590 DOI: 10.2174/0929867324666171106160326] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 08/31/2017] [Accepted: 10/30/2017] [Indexed: 12/12/2022]
Abstract
BACKGROUND Antimicrobial resistance is found in all microorganisms and has become one of the biggest threats to global health. New antimicrobials with different action mechanisms are effective weapons to fight against antibiotic-resistance. OBJECTIVE This review aims to find potential drugs which can be further developed into clinic practice and provide clues for developing more effective antimicrobials. METHODS DNA replication universally exists in all living organisms and is a complicated process in which multiple enzymes are involved in. Enzymes in bacterial DNA replication of initiation and elongation phases bring abundant targets for antimicrobial development as they are conserved and indispensable. In this review, enzyme inhibitors of DNA helicase, DNA primase, topoisomerases, DNA polymerase and DNA ligase were discussed. Special attentions were paid to structures, activities and action modes of these enzyme inhibitors. RESULTS Among these enzymes, type II topoisomerase is the most validated target with abundant inhibitors. For type II topoisomerase inhibitors (excluding quinolones), NBTIs and benzimidazole urea derivatives are the most promising inhibitors because of their good antimicrobial activity and physicochemical properties. Simultaneously, DNA gyrase targeted drugs are particularly attractive in the treatment of tuberculosis as DNA gyrase is the sole type II topoisomerase in Mycobacterium tuberculosis. Relatively, exploitation of antimicrobial inhibitors of the other DNA replication enzymes are primeval, in which inhibitors of topo III are even blank so far. CONCLUSION This review demonstrates that inhibitors of DNA replication enzymes are abundant, diverse and promising, many of which can be developed into antimicrobials to deal with antibioticresistance.
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Affiliation(s)
- Lanhua Yi
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Xin Lü
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province 712100, China
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24
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Das S, Garg T, Srinivas N, Dasgupta A, Chopra S. Targeting DNA Gyrase to Combat Mycobacterium tuberculosis: An Update. Curr Top Med Chem 2019; 19:579-593. [PMID: 30834837 DOI: 10.2174/1568026619666190304130218] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 10/10/2018] [Accepted: 01/02/2019] [Indexed: 11/22/2022]
Abstract
DNA gyrase is a clinically validated drug target, currently targeted only by fluoroquinolone class of antibacterials. However, owing to increasing drug resistance as well as a concomitant reduction in the availability of newer classes of antibiotics, fluoroquinolones are increasingly being over-utilized in order to treat serious infections, including multi-drug resistant tuberculosis. This, in turn, increases the probability of resistance to fluoroquinolones, which is mediated by a single amino acid change in gyrA, leading to class-wide resistance. In this review, we provide an overview of the recent progress in identifying novel scaffolds which target DNA gyrase and provide an update on their discovery and development status.
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Affiliation(s)
- Swetarka Das
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow-226031, Uttar Pradesh, India
| | - Tanu Garg
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow-226031, Uttar Pradesh, India
| | - Nanduri Srinivas
- Department of Medicinal and Process Chemistry, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana, India
| | - Arunava Dasgupta
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow-226031, Uttar Pradesh, India
| | - Sidharth Chopra
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow-226031, Uttar Pradesh, India
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25
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Hadži S, Kocman V, Oblak D, Plavec J, Lah J. Energetic Basis of AGCGA-Rich DNA Folding into a Tetrahelical Structure. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201813502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- San Hadži
- Faculty of Chemistry and Chemical Technology; University of Ljubljana; Večna pot 113 Ljubljana Slovenia
| | - Vojč Kocman
- National Institute of Chemistry; Hajdrihova 19 Slovenia
| | - Domen Oblak
- Faculty of Chemistry and Chemical Technology; University of Ljubljana; Večna pot 113 Ljubljana Slovenia
| | - Janez Plavec
- Faculty of Chemistry and Chemical Technology; University of Ljubljana; Večna pot 113 Ljubljana Slovenia
- National Institute of Chemistry; Hajdrihova 19 Slovenia
| | - Jurij Lah
- Faculty of Chemistry and Chemical Technology; University of Ljubljana; Večna pot 113 Ljubljana Slovenia
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The Anticancer Activities of Some Nitrogen Donor Ligands Containing bis-Pyrazole, Bipyridine, and Phenanthroline Moiety Using Docking Methods. Bioinorg Chem Appl 2018; 2018:5796287. [PMID: 29967635 PMCID: PMC6008838 DOI: 10.1155/2018/5796287] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Revised: 11/08/2017] [Accepted: 05/09/2018] [Indexed: 11/17/2022] Open
Abstract
The anticancer study of nitrogen-chelating ligands can be of tremendous help in choosing ligands for the anticancer metal complexes design especially with ruthenium(II). The inhibitory anticancer activities of some nitrogen-chelating ligands containing bis-pyrazole, bipyridine, and phenanthroline were studied using experimental screening against cancer cell and theoretical docking methods. In vitro anticancer activities showed compound 11 as the most promising inhibitor, and the computational docking further indicates its strong inhibitory activities towards some cancer-related receptors. Among the twenty-one modelled ligands, pyrazole-based compounds 7, 11, and 15 are the most promising inhibitors against the selected receptors followed by 18 and 21 which are derivatives of pyridine and phenanthroline, respectively. The presence of the carboxylic unit in the top five ligands that displayed stronger inhibitory activities against the selected receptors is an indication that the formation of noncovalent interactions such as hydrogen bonding and a strong electron-withdrawing group in these compounds are very important for their receptor interactions. The thermodynamic properties, the polarizabilities, and the LUMO energy of the compounds are in the same patterns as the observed inhibitory activities.
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Huang X, Guo J, Liu Q, Gu Q, Xu J, Zhou H. Identification of an auxiliary druggable pocket in the DNA gyrase ATPase domain using fragment probes. MEDCHEMCOMM 2018; 9:1619-1629. [PMID: 30429968 DOI: 10.1039/c8md00148k] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 07/03/2018] [Indexed: 12/21/2022]
Abstract
Discovery of new drug binding sites on well-established targets is of great interest as it facilitates the design of new mechanistic inhibitors to overcome the acquired drug resistance. Small chemical fragments can easily enter and bind to the cavities on the protein surface. Thus, they can be used to probe new druggable pockets in proteins. DNA gyrase plays indispensable roles in DNA replication, and both its GyrA and GyrB subunits are clinically validated antibacterial targets. New mechanistic GyrB inhibitors are urgently desired since the withdrawal of novobiocin from the market by the FDA due to its reduced efficiency and other reasons. Here, a fragment library was screened against the E. coli GyrB ATPase domain by combining affinity- and bioactivity-based approaches. The following X-ray crystallographic efforts were made to determine the cocrystal structures of GyrB with ten fragment hits, and three different binding modes were disclosed. Fortunately, a hydrophobic pocket which is previously unknown was identified by two fragments. Fragments that bind to this pocket were shown to inhibit the ATPase activity as well as the DNA topological transition activity of DNA gyrase in vitro. A set of fragment analogs were screened to explore the binding capacity of this pocket and identify the better starting fragments for lead development. Phylogenetic analysis revealed that this pocket is conserved in most Gram-negative and also many Gram-positive human pathogenic bacteria, implying a broad-spectrum antibacterial potential and a lower risk of mutation. Thus, the novel druggable pocket and the starting fragments provide a novel basis for designing new GyrB-targeting therapeutics.
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Affiliation(s)
- Xiaojie Huang
- Research Center for Drug Discovery , School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou 510006 , China .
| | - Junsong Guo
- Research Center for Drug Discovery , School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou 510006 , China .
| | - Qi Liu
- Research Center for Drug Discovery , School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou 510006 , China .
| | - Qiong Gu
- Research Center for Drug Discovery , School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou 510006 , China .
| | - Jun Xu
- Research Center for Drug Discovery , School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou 510006 , China .
| | - Huihao Zhou
- Research Center for Drug Discovery , School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou 510006 , China .
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Abstract
New antibacterials that modulate less explored targets are needed to fight the emerging bacterial resistance. DNA gyrase and topoisomerase IV are attractive targets in this search. These are both type II topoisomerases that can cleave both DNA strands, and can thus alter DNA topology during replication or similar processes. Currently, there are no ATP-competitive inhibitors of these two enzymes on the market, as the only aminocoumarin representative, novobiocin, was withdrawn due to safety concerns. The search for novel ATP-competitive inhibitors is a focus of ongoing industrial and academical research. This review summarizes the recent efforts in the design, synthesis and evaluation of GyrB/ParE inhibitors. The various approaches to achieve improved antibacterial activities are described, with particular reference to Gram-negative bacteria.
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Abdizadeh H, Tamer YT, Acar O, Toprak E, Atilgan AR, Atilgan C. Increased substrate affinity in the Escherichia coli L28R dihydrofolate reductase mutant causes trimethoprim resistance. Phys Chem Chem Phys 2018; 19:11416-11428. [PMID: 28422217 DOI: 10.1039/c7cp01458a] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dihydrofolate reductase (DHFR) is a ubiquitous enzyme with an essential role in cell metabolism. DHFR catalyzes the reduction of dihydrofolate to tetrahydrofolate, which is a precursor for purine and thymidylate synthesis. Several DHFR targeting antifolate drugs including trimethoprim, a competitive antibacterial inhibitor, have therefore been developed and are clinically used. Evolution of resistance against antifolates is a common public health problem rendering these drugs ineffective. To combat the resistance problem, it is important to understand resistance-conferring changes in the DHFR structure and accordingly develop alternative strategies. Here, we structurally and dynamically characterize Escherichia coli DHFR in its wild type (WT) and trimethoprim resistant L28R mutant forms in the presence of the substrate and its inhibitor trimethoprim. We use molecular dynamics simulations to determine the conformational space, loop dynamics and hydrogen bond distributions at the active site of DHFR for the WT and the L28R mutant. We also report their experimental kcat, Km, and Ki values, accompanied by isothermal titration calorimetry measurements of DHFR that distinguish enthalpic and entropic contributions to trimethoprim binding. Although mutations that confer resistance to competitive inhibitors typically make enzymes more promiscuous and decrease affinity to both the substrate and the inhibitor, strikingly, we find that the L28R mutant has a unique resistance mechanism. While the binding affinity differences between the WT and the mutant for the inhibitor and the substrate are small, the newly formed extra hydrogen bonds with the aminobenzoyl glutamate tail of DHF in the L28R mutant leads to increased barriers for the dissociation of the substrate and the product. Therefore, the L28R mutant indirectly gains resistance by enjoying prolonged binding times in the enzyme-substrate complex. While this also leads to slower product release and decreases the catalytic rate of the L28R mutant, the overall effect is the maintenance of a sufficient product formation rate. Finally, the experimental and computational analyses together reveal the changes that occur in the energetic landscape of DHFR upon the resistance-conferring L28R mutation. We show that the negative entropy associated with the binding of trimethoprim in WT DHFR is due to water organization at the binding interface. Our study lays the framework to study structural changes in other trimethoprim resistant DHFR mutants.
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Affiliation(s)
- Haleh Abdizadeh
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey.
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30
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Serratos IN, Millán-Pacheco C, Garza-Ramos G, Pérez-Hernández G, Zubillaga RA. Exploring interfacial water trapping in protein-ligand complexes with multithermal titration calorimetry. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:488-495. [PMID: 29307720 DOI: 10.1016/j.bbapap.2018.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 12/02/2017] [Accepted: 01/03/2018] [Indexed: 11/18/2022]
Abstract
In this work, we examine the hypothesis about how trapped water molecules at the interface between triosephosphate isomerase (TIM) and either of two phosphorylated inhibitors, 2-phosphoglycolate (2PG) or phosphoglycolohydroxamate (PGH), can explain the anomalous highly negative binding heat capacities (ΔCp,b) of both complexes, TIM-2PG and TIM-PGH. We performed fluorimetric titrations of the enzyme with PGH inhibitor under osmotic stress conditions, using various concentrations of either osmolyte: sucrose, ethylene glycol or glycine betaine. We also analyze the binding processes under various stressor concentrations using a novel calorimetric methodology that allows ΔCp,b determinations in single experiments: Multithermal Titration Calorimetry. The binding constant of the TIM-PGH complex decreased gradually with the concentration of all osmolytes, but at diverse extents depending on the osmolyte nature. According to the osmotic stress theory, this decrease indicates that the number of water molecules associated with the enzyme increases with inhibitor binding, i.e. some solvent molecules became trapped. Additionally, the binding heat capacities became less negative at higher osmolyte concentrations, their final values depending on the osmolyte. These effects were also observed in the TIM-2PG complex using sucrose as stressor. Our results strongly suggest that some water molecules became immobilized when the TIM-inhibitor complexes were formed. A computational analysis of the hydration state of the binding site of TIM in both its free state and its complexed form with 2PG or PGH, based on molecular dynamics (MD) simulations in explicit solvent, showed that the binding site effectively immobilized additional water molecules after binding these inhibitors.
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Affiliation(s)
- Iris N Serratos
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Ciudad de México, C.P. 09340, Mexico.
| | - Cesar Millán-Pacheco
- Facultad de Farmacia. Universidad Autónoma del Estado de Morelos, Cuernavaca Mor. C.P. 62209, Mexico.
| | - Georgina Garza-Ramos
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México C.P. 04510, Mexico.
| | - Gerardo Pérez-Hernández
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa, Ciudad de México, C.P. 05348, Mexico.
| | - Rafael A Zubillaga
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Ciudad de México, C.P. 09340, Mexico.
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31
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Regioselective glycosylation of novobiocin alters activity. Carbohydr Res 2017; 452:116-121. [DOI: 10.1016/j.carres.2017.10.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 10/13/2017] [Accepted: 10/18/2017] [Indexed: 01/13/2023]
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Panchaud P, Bruyère T, Blumstein AC, Bur D, Chambovey A, Ertel EA, Gude M, Hubschwerlen C, Jacob L, Kimmerlin T, Pfeifer T, Prade L, Seiler P, Ritz D, Rueedi G. Discovery and Optimization of Isoquinoline Ethyl Ureas as Antibacterial Agents. J Med Chem 2017; 60:3755-3775. [DOI: 10.1021/acs.jmedchem.6b01834] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Philippe Panchaud
- Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Thierry Bruyère
- Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | | | - Daniel Bur
- Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Alain Chambovey
- Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Eric A. Ertel
- Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Markus Gude
- Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | | | - Loïc Jacob
- Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Thierry Kimmerlin
- Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Thomas Pfeifer
- Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Lars Prade
- Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Peter Seiler
- Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Daniel Ritz
- Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Georg Rueedi
- Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
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33
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Erlitzki N, Huang K, Xhani S, Farahat AA, Kumar A, Boykin DW, Poon GMK. Investigation of the electrostatic and hydration properties of DNA minor groove-binding by a heterocyclic diamidine by osmotic pressure. Biophys Chem 2017; 231:95-104. [PMID: 28363467 DOI: 10.1016/j.bpc.2017.02.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Revised: 02/18/2017] [Accepted: 02/21/2017] [Indexed: 12/29/2022]
Abstract
Previous investigations of sequence-specific DNA binding by model minor groove-binding compounds showed that the ligand/DNA complex was destabilized in the presence of compatible co-solutes. Inhibition was interpreted in terms of osmotic stress theory as the uptake of significant numbers of excess water molecules from bulk solvent upon complex formation. Here, we interrogated the AT-specific DNA complex formed with the symmetric heterocyclic diamidine DB1976 as a model for minor groove DNA recognition using both ionic (NaCl) and non-ionic cosolutes (ethylene glycol, glycine betaine, maltose, nicotinamide, urea). While the non-ionic cosolutes all destabilized the ligand/DNA complex, their quantitative effects were heterogeneous in a cosolute- and salt-dependent manner. Perturbation with NaCl in the absence of non-ionic cosolute showed that preferential hydration water was released upon formation of the DB1976/DNA complex. As salt probes counter-ion release from charged groups such as the DNA backbone, we propose that the preferential hydration uptake in DB1976/DNA binding observed in the presence of osmolytes reflects the exchange of preferentially bound cosolute with hydration water in the environs of the bound DNA, rather than a net uptake of hydration waters by the complex.
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Affiliation(s)
- Noa Erlitzki
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - Kenneth Huang
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - Suela Xhani
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - Abdelbasset A Farahat
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States; Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Arvind Kumar
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - David W Boykin
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - Gregory M K Poon
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, United States.
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34
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Harish B, Swapna GVT, Kornhaber GJ, Montelione GT, Carey J. Multiple helical conformations of the helix-turn-helix region revealed by NOE-restrained MD simulations of tryptophan aporepressor, TrpR. Proteins 2017; 85:731-740. [PMID: 28120439 DOI: 10.1002/prot.25252] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 12/20/2016] [Accepted: 01/04/2017] [Indexed: 11/11/2022]
Abstract
The nature of flexibility in the helix-turn-helix region of E. coli trp aporepressor has been unexplained for many years. The original ensemble of nuclear magnetic resonance (NMR structures showed apparent disorder, but chemical shift and relaxation measurements indicated a helical region. Nuclear Overhauser effect (NOE) data for a temperature-sensitive mutant showed more helical character in its helix-turn-helix region, but nevertheless also led to an apparently disordered ensemble. However, conventional NMR structure determination methods require all structures in the ensemble to be consistent with every NOE simultaneously. This work uses an alternative approach in which some structures of the ensemble are allowed to violate some NOEs to permit modeling of multiple conformational states that are in dynamic equilibrium. Newly measured NOE data for wild-type aporepressor are used as time-averaged distance restraints in molecular dynamics simulations to generate an ensemble of helical conformations that is more consistent with the observed NMR data than the apparent disorder in the previously reported NMR structures. The results indicate the presence of alternating helical conformations that provide a better explanation for the flexibility of the helix-turn-helix region of trp aporepressor. Structures representing these conformations have been deposited with PDB ID: 5TM0. Proteins 2017; 85:731-740. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
| | - G V T Swapna
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854
| | - Gregory J Kornhaber
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854
| | - Gaetano T Montelione
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854.,Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854
| | - Jannette Carey
- Chemistry Department, Princeton University, Princeton, New Jersey, 08544
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35
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Wear MA, Nowicki MW, Blackburn EA, McNae IW, Walkinshaw MD. Thermo-kinetic analysis space expansion for cyclophilin-ligand interactions - identification of a new nonpeptide inhibitor using Biacore™ T200. FEBS Open Bio 2017; 7:533-549. [PMID: 28396838 PMCID: PMC5377415 DOI: 10.1002/2211-5463.12201] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 01/18/2017] [Accepted: 01/23/2017] [Indexed: 12/31/2022] Open
Abstract
We have established a refined methodology for generating surface plasmon resonance sensor surfaces of recombinant his‐tagged human cyclophilin‐A. Our orientation‐specific stabilisation approach captures his‐tagged protein under ‘physiological conditions’ (150 mm NaCl, pH 7.5) and covalently stabilises it on Ni2+‐nitrilotriacetic acid surfaces, very briefly activated for primary amine‐coupling reactions, producing very stable and active surfaces (≥ 95% specific activity) of cyclophilin‐A. Variation in protein concentration with the same contact time allows straightforward generation of variable density surfaces, with essentially no loss of activity, making the protocol easily adaptable for studying numerous interactions; from very small fragments, ~ 100 Da, to large protein ligands. This new method results in an increased stability and activity of the immobilised protein and allowed us to expand the thermo‐kinetic analysis space, and to determine accurate and robust thermodynamic parameters for the cyclophilin‐A–cyclosporin‐A interaction. Furthermore, the increased sensitivity of the surface allowed identification of a new nonpeptide inhibitor of cyclophilin‐A, from a screen of a fragment library. This fragment, 2,3‐diaminopyridine, bound specifically with a mean affinity of 248 ± 60 μm. The X‐ray structure of this 109‐Da fragment bound in the active site of cyclophilin‐A was solved to a resolution of 1.25 Å (PDB: 5LUD), providing new insight into the molecular details for a potential new series of nonpeptide cyclophilin‐A inhibitors.
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Affiliation(s)
- Martin A Wear
- The Edinburgh Protein Production Facility (EPPF) Wellcome Trust Centre for Cell Biology (WTCCB) University of Edinburgh UK
| | - Matthew W Nowicki
- The Edinburgh Protein Production Facility (EPPF) Wellcome Trust Centre for Cell Biology (WTCCB) University of Edinburgh UK
| | - Elizabeth A Blackburn
- The Edinburgh Protein Production Facility (EPPF) Wellcome Trust Centre for Cell Biology (WTCCB) University of Edinburgh UK
| | - Iain W McNae
- The Edinburgh Protein Production Facility (EPPF) Wellcome Trust Centre for Cell Biology (WTCCB) University of Edinburgh UK
| | - Malcolm D Walkinshaw
- The Edinburgh Protein Production Facility (EPPF) Wellcome Trust Centre for Cell Biology (WTCCB) University of Edinburgh UK
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36
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Zhang M, Zhang R, Wang J, Yu X, Zhang Y, Wang Q, Zhang W. Microwave-promoted Synthesis of Novel Fused Osthole Analogues. CHINESE J CHEM 2016. [DOI: 10.1002/cjoc.201600489] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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37
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Linker-switch approach towards new ATP binding site inhibitors of DNA gyrase B. Eur J Med Chem 2016; 125:500-514. [PMID: 27689732 DOI: 10.1016/j.ejmech.2016.09.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 08/18/2016] [Accepted: 09/13/2016] [Indexed: 12/30/2022]
Abstract
Due to increasing emergence of bacterial resistance, compounds with new mechanisms of action are of paramount importance. One of modestly researched therapeutic targets in the field of antibacterial discovery is DNA gyrase B. In the present work we synthesized a focused library of potential DNA gyrase B inhibitors composed of two key pharmacophoric moieties linked by three types of sp3-rich linkers to obtain three structural classes of compounds. Using molecular docking, molecular dynamics and analysis of conserved waters in the binding site, we identified a favourable binding mode for piperidin-4-yl and 4-cyclohexyl pyrrole-2-carboxamides while predicting unfavourable interactions with the active site for piperazine pyrrole-2-carboxamides. Biological evaluation of prepared compounds on isolated enzyme DNA gyrase B confirmed our predictions and afforded multiple moderately potent inhibitors of DNA gyrase B. Namely trans-4-(4,5-dibromo-1H-pyrrole-2-carboxamide)cyclohexyl)glycine and 4-(4-(3,4-dichloro-5-methyl-1H-pyrrole-2-carboxamido)piperidin-1-yl)-4-oxobutanoic acid with an IC50 value of 16 and 0.5 μM respectively.
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38
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Snow Setzer M, Sharifi-Rad J, Setzer WN. The Search for Herbal Antibiotics: An In-Silico Investigation of Antibacterial Phytochemicals. Antibiotics (Basel) 2016; 5:E30. [PMID: 27626453 PMCID: PMC5039526 DOI: 10.3390/antibiotics5030030] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 08/14/2016] [Accepted: 08/26/2016] [Indexed: 01/12/2023] Open
Abstract
Recently, the emergence and spread of pathogenic bacterial resistance to many antibiotics (multidrug-resistant strains) have been increasing throughout the world. This phenomenon is of great concern and there is a need to find alternative chemotherapeutic agents to combat these antibiotic-resistant microorganisms. Higher plants may serve as a resource for new antimicrobials to replace or augment current therapeutic options. In this work, we have carried out a molecular docking study of a total of 561 antibacterial phytochemicals listed in the Dictionary of Natural Products, including 77 alkaloids (17 indole alkaloids, 27 isoquinoline alkaloids, 4 steroidal alkaloids, and 28 miscellaneous alkaloids), 99 terpenoids (5 monoterpenoids, 31 sesquiterpenoids, 52 diterpenoids, and 11 triterpenoids), 309 polyphenolics (87 flavonoids, 25 chalcones, 41 isoflavonoids, 5 neoflavonoids, 12 pterocarpans, 10 chromones, 7 condensed tannins, 11 coumarins, 30 stilbenoids, 2 lignans, 5 phenylpropanoids, 13 xanthones, 5 hydrolyzable tannins, and 56 miscellaneous phenolics), 30 quinones, and 46 miscellaneous phytochemicals, with six bacterial protein targets (peptide deformylase, DNA gyrase/topoisomerase IV, UDP-galactose mutase, protein tyrosine phosphatase, cytochrome P450 CYP121, and NAD⁺-dependent DNA ligase). In addition, 35 known inhibitors were docked with their respective targets for comparison purposes. Prenylated polyphenolics showed the best docking profiles, while terpenoids had the poorest. The most susceptible protein targets were peptide deformylases and NAD⁺-dependent DNA ligases.
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Affiliation(s)
- Mary Snow Setzer
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA.
| | - Javad Sharifi-Rad
- Zabol Medicinal Plants Research Center, Zabol University of Medical Sciences, Zabol 61615-585, Iran.
- Department of Pharmacognosy, Zabol University of Medical Sciences, Zabol 61615-585, Iran.
| | - William N Setzer
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA.
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39
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Fang Y, Lu Y, Zang X, Wu T, Qi X, Pan S, Xu X. 3D-QSAR and docking studies of flavonoids as potent Escherichia coli inhibitors. Sci Rep 2016; 6:23634. [PMID: 27049530 PMCID: PMC4822154 DOI: 10.1038/srep23634] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 03/10/2016] [Indexed: 02/08/2023] Open
Abstract
Flavonoids are potential antibacterial agents. However, key substituents and mechanism for their antibacterial activity have not been fully investigated. The quantitative structure-activity relationship (QSAR) and molecular docking of flavonoids relating to potent anti-Escherichia coli agents were investigated. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were developed by using the pIC50 values of flavonoids. The cross-validated coefficient (q(2)) values for CoMFA (0.743) and for CoMSIA (0.708) were achieved, illustrating high predictive capabilities. Selected descriptors for the CoMFA model were ClogP (logarithm of the octanol/water partition coefficient), steric and electrostatic fields, while, ClogP, electrostatic and hydrogen bond donor fields were used for the CoMSIA model. Molecular docking results confirmed that half of the tested flavonoids inhibited DNA gyrase B (GyrB) by interacting with adenosine-triphosphate (ATP) pocket in a same orientation. Polymethoxyl flavones, flavonoid glycosides, isoflavonoids changed their orientation, resulting in a decrease of inhibitory activity. Moreover, docking results showed that 3-hydroxyl, 5-hydroxyl, 7-hydroxyl and 4-carbonyl groups were found to be crucial active substituents of flavonoids by interacting with key residues of GyrB, which were in agreement with the QSAR study results. These results provide valuable information for structure requirements of flavonoids as antibacterial agents.
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Affiliation(s)
- Yajing Fang
- Key Laboratory of Environment Correlative Dietology (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, P.R. China
| | - Yulin Lu
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Xixi Zang
- Oilcrops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, P.R. China
| | - Ting Wu
- Key Laboratory of Environment Correlative Dietology (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, P.R. China
| | - XiaoJuan Qi
- College of Science, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Siyi Pan
- Key Laboratory of Environment Correlative Dietology (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, P.R. China
| | - Xiaoyun Xu
- Key Laboratory of Environment Correlative Dietology (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, P.R. China
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Zidar N, Macut H, Tomašič T, Brvar M, Montalvão S, Tammela P, Solmajer T, Peterlin Mašič L, Ilaš J, Kikelj D. N-Phenyl-4,5-dibromopyrrolamides and N-Phenylindolamides as ATP Competitive DNA Gyrase B Inhibitors: Design, Synthesis, and Evaluation. J Med Chem 2015; 58:6179-94. [PMID: 26126187 DOI: 10.1021/acs.jmedchem.5b00775] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Bacterial DNA gyrase is a well-known and validated target in the design of antibacterial drugs. However, inhibitors of its ATP binding subunit, DNA gyrase B (GyrB), have so far not reached clinical use. In the present study, three different series of N-phenyl-4,5-dibromopyrrolamides and N-phenylindolamides were designed and prepared as potential DNA gyrase B inhibitors. The IC50 values of compounds on DNA gyrase from Escherichia coli were in the low micromolar range, with the best compound, (4-(4,5-dibromo-1H-pyrrole-2-carboxamido)benzoyl)glycine (18a), displaying an IC50 of 450 nM. For this compound, a high-resolution crystal structure in complex with E. coli DNA gyrase B was obtained, revealing details of its binding mode within the active site. The binding affinities of three compounds with GyrB were additionally evaluated by surface plasmon resonance, and the results were in good agreement with the determined enzymatic activities. For the most promising compounds, the inhibitory activities against DNA gyrase from Staphylococcus aureus and topoisomerases IV from E. coli and S. aureus were determined. Antibacterial activities of the most potent compounds of each series were evaluated against two Gram-positive and two Gram-negative bacterial strains. The results obtained in this study provide valuable information on the binding mode and structure-activity relationship of N-phenyl-4,5-dibromopyrrolamides and N-phenylindolamides as promising classes of ATP competitive GyrB inhibitors.
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Affiliation(s)
- Nace Zidar
- †Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Helena Macut
- †Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Tihomir Tomašič
- †Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Matjaž Brvar
- ‡National Institute of Chemistry, Laboratory for Biocomputing and Bioinformatics, 1001 Ljubljana, Slovenia
| | - Sofia Montalvão
- §Centre for Drug Research, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), Helsinki FI-00014, Finland
| | - Päivi Tammela
- §Centre for Drug Research, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), Helsinki FI-00014, Finland
| | - Tom Solmajer
- ‡National Institute of Chemistry, Laboratory for Biocomputing and Bioinformatics, 1001 Ljubljana, Slovenia
| | - Lucija Peterlin Mašič
- †Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Janez Ilaš
- †Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Danijel Kikelj
- †Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
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Kumar D, Poornima M, Kushwaha RN, Won TJ, Ahn C, Ganesh Kumar C, Jang K, Shin DS. Antimicrobial and docking studies of (−)-catechin derivatives. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/s13765-015-0079-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Ghatak T, Sarkar M, Dinda S, Dutta I, Rahaman SMW, Bera JK. Olefin Oxygenation by Water on an Iridium Center. J Am Chem Soc 2015; 137:6168-71. [DOI: 10.1021/jacs.5b03055] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tapas Ghatak
- Department of Chemistry and
Center for Environmental Science and Engineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Mithun Sarkar
- Department of Chemistry and
Center for Environmental Science and Engineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Shrabani Dinda
- Department of Chemistry and
Center for Environmental Science and Engineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Indranil Dutta
- Department of Chemistry and
Center for Environmental Science and Engineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - S. M. Wahidur Rahaman
- Department of Chemistry and
Center for Environmental Science and Engineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Jitendra K. Bera
- Department of Chemistry and
Center for Environmental Science and Engineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
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Abstract
DNA topoisomerases are enzymes that control the topology of DNA in all cells. There are two types, I and II, classified according to whether they make transient single- or double-stranded breaks in DNA. Their reactions generally involve the passage of a single- or double-strand segment of DNA through this transient break, stabilized by DNA-protein covalent bonds. All topoisomerases can relax DNA, but DNA gyrase, present in all bacteria, can also introduce supercoils into DNA. Because of their essentiality in all cells and the fact that their reactions proceed via DNA breaks, topoisomerases have become important drug targets; the bacterial enzymes are key targets for antibacterial agents. This article discusses the structure and mechanism of topoisomerases and their roles in the bacterial cell. Targeting of the bacterial topoisomerases by inhibitors, including antibiotics in clinical use, is also discussed.
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Nagano S, Lin TY, Edula JR, Heddle JG. Unique features of apicoplast DNA gyrases from Toxoplasma gondii and Plasmodium falciparum. BMC Bioinformatics 2014; 15:416. [PMID: 25523502 PMCID: PMC4297366 DOI: 10.1186/s12859-014-0416-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 12/10/2014] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND DNA gyrase, an enzyme once thought to be unique to bacteria, is also found in some eukaryotic plastids including the apicoplast of Apicomplexa such as Plasmodium falciparum and Toxoplasma gondii which are important disease-causing organisms. DNA gyrase is an excellent target for antibacterial drugs, yet such antibacterials seem ineffective against Apicomplexa. Characterisation of the apicoplast gyrases would be a useful step towards understanding why this should be so. While purification of active apicoplast gyrase has proved impossible to date, in silico analyses have allowed us to discover differences in the apicoplast proteins. The resulting predicted structural and functional differences will be a first step towards development of apicoplast-gyrase specific inhibitors. RESULTS We have carried out sequence analysis and structural predictions of the enzymes from the two species and find that P. falciparum gyrase lacks a GyrA box, but T. gondii may retain one. All proteins contained signal/transport peptides for localization to the apicoplast but T. gondii Gyrase B protein lacks the expected hydrophobic region. The most significant difference is in the GyrA C-terminal domain: While the cores of the proteins, including DNA binding and cleavage regions are essentially unchanged, both apicoplast gyrase A proteins have C-terminal domains that are significantly larger than bacterial counterparts and are predicted to have different structures. CONCLUSION The apicoplast gyrases differ significantly from bacterial gyrases while retaining similar core domains. T. gondii Gyrase B may have an unusual or inefficient mechanism of localisation to the apicoplast. P.falciparum gyrase, lacks a GyrA box and is therefore likely to be inefficient in DNA supercoiling. The C-terminal domains of both apicoplast Gyrase A proteins diverge significantly from the bacterial proteins. We predict that an additional structural element is present in the C-terminal domain of both apicoplast Gyrase A proteins, including the possibility of a β-pinwheel with a non-canonical number of blades. These differences undoubtedly will affect the DNA supercoiling mechanism and have perhaps evolved to compensate for the lack of Topoisomerase IV in the apicoplast. These data will be useful first step towards further characterisation and development of inhibitors for apicoplast gyrases.
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Affiliation(s)
- Soshichiro Nagano
- Heddle Initiative Research Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
| | - Ting-Yu Lin
- Heddle Initiative Research Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
| | - Jyotheeswara Reddy Edula
- Heddle Initiative Research Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. .,Current address: Department of Molecular Protozoology, Research Institute for Microbial Diseases (RIMD), Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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Thermodynamics and solvent linkage of macromolecule-ligand interactions. Methods 2014; 76:51-60. [PMID: 25462561 DOI: 10.1016/j.ymeth.2014.11.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 11/11/2014] [Accepted: 11/13/2014] [Indexed: 02/06/2023] Open
Abstract
Binding involves two steps, desolvation and association. While water is ubiquitous and occurs at high concentration, it is typically ignored. In vitro experiments typically use infinite dilution conditions, while in vivo, the concentration of water is decreased due to the presence of high concentrations of molecules in the cellular milieu. This review discusses isothermal titration calorimetry approaches that address the role of water in binding. For example, use of D2O allows the contribution of solvent reorganization to the enthalpy component to be assessed. Further, the addition of osmolytes will decrease the water activity of a solution and allow effects on Ka to be determined. In most cases, binding becomes tighter in the presence of osmolytes as the desolvation penalty associated with binding is minimized. In other cases, the osmolytes prefer to interact with the ligand or protein, and if their removal is more difficult than shedding water, then binding can be weakened. These complicating layers can be discerned by different slopes in ln(Ka) vs osmolality plots and by differential scanning calorimetry in the presence of the osmolyte.
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Humnabadkar V, Madhavapeddi P, Basavarajappa H, Sheikh MG, Rane R, Basu R, Verma P, Sundaram A, Mukherjee K, de Sousa SM. Assays, Surrogates, and Alternative Technologies for a TB Lead Identification Program Targeting DNA Gyrase ATPase. ACTA ACUST UNITED AC 2014; 20:265-74. [DOI: 10.1177/1087057114554170] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Mycobacterium tuberculosis (Mtb) DNA gyrase ATPase was the target of a tuberculosis drug discovery program. The low specific activity of the Mtb ATPase prompted the use of Mycobacterium smegmatis (Msm) enzyme as a surrogate for lead generation, since it had 20-fold higher activity. Addition of GyrA or DNA did not significantly increase the activity of the Msm GyrB ATPase, and an assay was developed using GyrB alone. Inhibition of the Msm ATPase correlated well with inhibition of Mtb DNA gyrase supercoiling across three chemical scaffolds, justifying its use. As the IC50 of compounds approached the enzyme concentration, surrogate assays were used to estimate potencies (e.g., the shift in thermal melt of Mtb GyrB, which correlated well with IC50s >10 nM). Analysis using the Morrison equation enabled determination of [Formula: see text]s in the sub-nanomolar range. Surface plasmon resonance was used to confirm these IC50s and measure the Kds of binding, but a fragment of Mtb GyrB had to be used. Across three scaffolds, the dissociation half life, t1/2, of the inhibitor-target complex was ≤8 min. This toolkit of assays was developed to track the potency of enzyme inhibition and guide the chemistry for progression of compounds in a lead identification program.
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Affiliation(s)
| | | | - Halesha Basavarajappa
- AstraZeneca India Pvt. Ltd., Bangalore, India
- Indiana University School of Medicine, Indianapolis, USA
| | - Md. Gulebahar Sheikh
- AstraZeneca India Pvt. Ltd., Bangalore, India
- Enzene Bioscience Ltd., Bangalore, India
| | | | | | | | | | - Kakoli Mukherjee
- AstraZeneca India Pvt. Ltd., Bangalore, India
- Alkem Laboratories, Bangalore, India
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Indrasena A, Riyaz S, Mallipeddi PL, Padmaja P, Sridhar B, Dubey P. Design, synthesis, and biological evaluation of indolylidinepyrazolones as potential anti-bacterial agents. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.05.131] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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48
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Tork Ladani S, Hamelberg D. Intricacies of interactions, dynamics and solvent effects in enzyme catalysis: a computational perspective on cyclophilin A. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.919498] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Suresh N, Nagesh HN, Renuka J, Rajput V, Sharma R, Khan IA, Kondapalli Venkata Gowri CS. Synthesis and evaluation of 1-cyclopropyl-6-fluoro-1,4-dihydro-4-oxo-7-(4-(2-(4-substitutedpiperazin-1-yl)acetyl)piperazin-1-yl)quinoline-3-carboxylic acid derivatives as anti-tubercular and antibacterial agents. Eur J Med Chem 2014; 71:324-32. [DOI: 10.1016/j.ejmech.2013.10.055] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 09/06/2013] [Accepted: 10/22/2013] [Indexed: 11/16/2022]
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50
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Ramos JP, Le VH, Lewis EA. Role of Water in Netropsin Binding to an A2T2 Hairpin DNA Site: Osmotic Stress Experiments. J Phys Chem B 2013; 117:15958-65. [DOI: 10.1021/jp408077m] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Joseph P. Ramos
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Vu H. Le
- Department
of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Edwin A. Lewis
- Department
of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
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