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Mendieta-Wejebe JE, Rosales-Hernández MC, Padilla-Martínez II, García-Báez EV, Cruz A. Design, Synthesis and Biological Activities of (Thio)Urea Benzothiazole Derivatives. Int J Mol Sci 2023; 24:9488. [PMID: 37298442 PMCID: PMC10253887 DOI: 10.3390/ijms24119488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/17/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
(Thio)ureas ((T)Us) and benzothiazoles (BTs) each have demonstrated to have a great variety of biological activities. When these groups come together, the 2-(thio)ureabenzothizoles [(T)UBTs] are formed, improving the physicochemical as well as the biological properties, making these compounds very interesting in medicinal chemistry. Frentizole, bentaluron and methabenzthiazuron are examples of UBTs used for treatment of rheumatoid arthritis and as wood preservatives and herbicides in winter corn crops, respectively. With this antecedent, we recently reported a bibliographic review about the synthesis of this class of compounds, from the reaction of substituted 2-aminobenzothiazoles (ABTs) with iso(thio)cyanates, (thio)phosgenes, (thio)carbamoyl chlorides, 1,1'-(thio)carbonyldiimidazoles, and carbon disulfide. Herein, we prepared a bibliographic review about those features of design, chemical synthesis, and biological activities relating to (T)UBTs as potential therapeutic agents. This review is about synthetic methodologies generated from 1968 to the present day, highlighting the focus to transform (T)UBTs to compounds containing a range substituents, as illustrated with 37 schemes and 11 figures and concluded with 148 references. In this topic, the scientists dedicated to medicinal chemistry and pharmaceutical industry will find useful information for the design and synthesis of this interesting group of compounds with the aim of repurposing these compounds.
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Affiliation(s)
- Jessica E. Mendieta-Wejebe
- Laboratorio de Biofísica y Biocatálisis, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón s/n, Casco de Santo Tomás, Ciudad de Mexico 11340, Mexico; (J.E.M.-W.); (M.C.R.-H.)
| | - Martha C. Rosales-Hernández
- Laboratorio de Biofísica y Biocatálisis, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón s/n, Casco de Santo Tomás, Ciudad de Mexico 11340, Mexico; (J.E.M.-W.); (M.C.R.-H.)
| | - Itzia I. Padilla-Martínez
- Laboratorio de Química Supramolecular y Nanociencias, Unidad Profesional Interdisciplinaria de Biotecnología, Instituto Politécnico Nacional, Av. Acueducto s/n, Barrio la Laguna Ticomán, Ciudad de Mexico 07340, Mexico; (I.I.P.-M.); (E.V.G.-B.)
| | - Efrén V. García-Báez
- Laboratorio de Química Supramolecular y Nanociencias, Unidad Profesional Interdisciplinaria de Biotecnología, Instituto Politécnico Nacional, Av. Acueducto s/n, Barrio la Laguna Ticomán, Ciudad de Mexico 07340, Mexico; (I.I.P.-M.); (E.V.G.-B.)
| | - Alejandro Cruz
- Laboratorio de Química Supramolecular y Nanociencias, Unidad Profesional Interdisciplinaria de Biotecnología, Instituto Politécnico Nacional, Av. Acueducto s/n, Barrio la Laguna Ticomán, Ciudad de Mexico 07340, Mexico; (I.I.P.-M.); (E.V.G.-B.)
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Sterle M, Huš M, Lozinšek M, Zega A, Cotman AE. Hydrogen-Bonding Ability of Noyori-Ikariya Catalysts Enables Stereoselective Access to CF 3-Substituted syn-1,2-Diols via Dynamic Kinetic Resolution. ACS Catal 2023; 13:6242-6248. [PMID: 37180962 PMCID: PMC10167654 DOI: 10.1021/acscatal.3c00980] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/06/2023] [Indexed: 05/16/2023]
Abstract
Stereopure CF3-substituted syn-1,2-diols were prepared via the reductive dynamic kinetic resolution of the corresponding racemic α-hydroxyketones in HCO2H/Et3N. (Het)aryl, benzyl, vinyl, and alkyl ketones are tolerated, delivering products with ≥95% ee and ≥87:13 syn/anti. This methodology offers rapid access to stereopure bioactive molecules. Furthermore, DFT calculations for three types of Noyori-Ikariya ruthenium catalysts were performed to show their general ability of directing stereoselectivity via the hydrogen bond acceptor SO2 region and CH/π interactions.
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Affiliation(s)
- Maša Sterle
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, SI-1000 Ljubljana, Slovenia
| | - Matej Huš
- National
Institute of Chemistry, Department of Catalysis
and Chemical Reaction Engineering, Hajdrihova ulica 19, SI-1000 Ljubljana, Slovenia
- Association
for Technical Culture of Slovenia, Zaloška cesta 65, SI-1000 Ljubljana, Slovenia
- Institute
for the Protection of Cultural Heritage of Slovenia, Poljanska 40, SI-1000 Ljubljana, Slovenia
| | - Matic Lozinšek
- Jožef
Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
| | - Anamarija Zega
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, SI-1000 Ljubljana, Slovenia
| | - Andrej Emanuel Cotman
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, SI-1000 Ljubljana, Slovenia
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3
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Rosales-Hernández MC, Mendieta-Wejebe JE, Padilla-Martínez II, García-Báez EV, Cruz A. Synthesis and Biological Importance of 2-(thio)ureabenzothiazoles. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27186104. [PMID: 36144837 PMCID: PMC9502297 DOI: 10.3390/molecules27186104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/11/2022] [Accepted: 09/14/2022] [Indexed: 11/22/2022]
Abstract
The (thio)urea and benzothiazole (BT) derivatives have been shown to have a broad spectrum of biological activities. These groups, when bonded, result in the 2-(thio)ureabenzothizoles (TBT and UBT), which could favor the physicochemical and biological properties. UBTs and TBTs are compounds of great importance in medicinal chemistry. For instance, Frentizole is a UBT derivative used for the treatment of rheumatoid arthritis and systemic lupus erythematosus. The UBTs Bentaluron and Bethabenthiazuron are commercial fungicides used as wood preservatives and herbicides in winter corn crops. On these bases, we prepared this bibliography review, which covers chemical aspects of UBTs and TBTs as potential therapeutic agents as well as their studies on the mechanisms of a variety of pharmacological activities. This work covers synthetic methodologies from 1935 to nowadays, highlighting the most recent approaches to afford UBTs and TBTs with a variety of substituents as illustrated in 42 schemes and 13 figures and concluded with 187 references. In addition, this interesting review is designed on chemical reactions of 2-aminobenzothiazoles (2ABTs) with (thio)phosgenes, iso(thio)cyanates, 1,1′-(thio)carbonyldiimidazoles [(T)CDI]s, (thio)carbamoyl chlorides, and carbon disulfide. This topic will provide information of utility for medicinal chemists dedicated to the design and synthesis of this class of compounds to be tested with respect to their biological activities and be proposed as new pharmacophores.
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Affiliation(s)
- Martha Cecilia Rosales-Hernández
- Laboratorio de Biofísica y Biocatálisis, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón s/n, Casco de Santo Tomás, Mexico City 11340, Mexico
| | - Jessica E. Mendieta-Wejebe
- Laboratorio de Biofísica y Biocatálisis, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón s/n, Casco de Santo Tomás, Mexico City 11340, Mexico
| | - Itzia I. Padilla-Martínez
- Instituto Politécnico Nacional-UPIBI, Laboratorio de Química Supramolecular y Nanociencias, Av. Acueducto s/n, Barrio la Laguna Ticomán, Mexico City 07340, Mexico
| | - Efrén V. García-Báez
- Instituto Politécnico Nacional-UPIBI, Laboratorio de Química Supramolecular y Nanociencias, Av. Acueducto s/n, Barrio la Laguna Ticomán, Mexico City 07340, Mexico
| | - Alejandro Cruz
- Instituto Politécnico Nacional-UPIBI, Laboratorio de Química Supramolecular y Nanociencias, Av. Acueducto s/n, Barrio la Laguna Ticomán, Mexico City 07340, Mexico
- Correspondence:
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A Novel Oral GyrB/ParE Dual Binding Inhibitor Effective against Multidrug-Resistant Neisseria gonorrhoeae and Other High-Threat Pathogens. Antimicrob Agents Chemother 2022; 66:e0041422. [PMID: 35972242 PMCID: PMC9487510 DOI: 10.1128/aac.00414-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Drug-resistant Neisseria gonorrhoeae is a serious global health concern. New drugs are needed that can overcome existing drug resistance and limit the development of new resistances. Here, we describe the small molecule tricyclic pyrimidoindole JSF-2414 [8-(6-fluoro-8-(methylamino)-2-((2-methylpyrimidin-5-yl)oxy)-9H-pyrimido[4,5-b]indol-4-yl)-2-oxa-8-azaspiro[4.5]decan-3-yl)methanol], which was developed to target both ATP-binding regions of DNA gyrase (GyrB) and topoisomerase (ParE). JSF-2414 displays potent activity against N. gonorrhoeae, including drug-resistant strains. A phosphate pro-drug, JSF-2659, was developed to facilitate oral dosing. In two different animal models of Neisseria gonorrhoeae vaginal infection, JSF-2659 was highly efficacious in reducing microbial burdens to the limit of detection. The parent molecule also showed potent in vitro activity against high-threat Gram-positive organisms, and JSF-2659 was shown in a deep tissue model of vancomycin-resistant Staphylococcus aureus (VRSA) and a model of Clostridioides difficile-induced colitis to be highly efficacious and protective. JSF-2659 is a novel preclinical drug candidate against high-threat multidrug resistant organisms with low potential to develop new resistance.
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Hugelshofer CL, Bao J, Du J, Ashley E, Yu W, Ji T, Hu B, Liu D, Rondla R, Karampuri S, Sharma V, Ethiraj K, Lim YH. Scalable Preparation of 4,4-Disubstituted Six-Membered Cyclic Sulfones. Org Lett 2021; 23:943-947. [PMID: 33417467 DOI: 10.1021/acs.orglett.0c04141] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We provide an account of synthetic strategies aimed at the efficient preparation of 4-amino-4-methyltetrahydro-2H-thiopyran 1,1-dioxide (3), an important cyclic sulfone building block for medicinal chemistry. A practical and scalable protocol has been developed that readily gives access to the title compound from commercially available and inexpensive starting materials. In addition, this novel approach has enabled the synthesis of various related 4,4-disubstituted cyclic sulfone derivatives that serve as valuable structural motifs for drug discovery.
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Affiliation(s)
- Cedric L Hugelshofer
- Department of Discovery Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Jianming Bao
- Department of Discovery Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Juana Du
- Process Research and Development, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Eric Ashley
- Process Research and Development, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Wensheng Yu
- External Discovery Chemistry, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Tao Ji
- IDSU, WuXi AppTec Co., Ltd., Shanghai 200131, China
| | - Bin Hu
- IDSU, WuXi AppTec Co., Ltd., Shanghai 200131, China
| | - Dejun Liu
- IDSU, WuXi AppTec Co., Ltd., Shanghai 200131, China
| | - Ramu Rondla
- GVK Biosciences Pvt, Ltd., Telangana 500076, India
| | | | | | | | - Yeon-Hee Lim
- Department of Discovery Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States
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6
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Importance of Fluorine in Benzazole Compounds. Molecules 2020; 25:molecules25204677. [PMID: 33066333 PMCID: PMC7587361 DOI: 10.3390/molecules25204677] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/15/2020] [Accepted: 09/18/2020] [Indexed: 12/31/2022] Open
Abstract
Fluorine-containing heterocycles continue to receive considerable attention due to their unique properties. In medicinal chemistry, the incorporation of fluorine in small molecules imparts a significant enhancement their biological activities compared to non-fluorinated molecules. In this short review, we will highlight the importance of incorporating fluorine as a basic appendage in benzothiazole and benzimidazole skeletons. The chemistry and pharmacological activities of heterocycles containing fluorine during the past years are compiled and discussed.
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7
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Exploitation of Pare Topoisomerase IV as Drug Target for the Treatment of Multidrug-Resistant Bacteria: A Review. Pharm Chem J 2020. [DOI: 10.1007/s11094-020-02223-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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8
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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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9
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Stokes SS, Vemula R, Pucci MJ. Advancement of GyrB Inhibitors for Treatment of Infections Caused by Mycobacterium tuberculosis and Non-tuberculous Mycobacteria. ACS Infect Dis 2020; 6:1323-1331. [PMID: 32183511 DOI: 10.1021/acsinfecdis.0c00025] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The prospect of ever increasing antibiotic resistance eroding currently available treatment options for bacterial infections underscores the need to continue to identify new antibiotics, preferably those that act on novel targets or with novel mechanisms of action. Bacterial gyrase B subunit (GyrB), an essential component of bacterial gyrase required for successful DNA replication, represents such a target. We describe recent examples of GyrB inhibitors and point out their potential utility for treatment of mycobacterial diseases caused by Mycobacterium tuberculosis (TB) and non-tuberculous mycobacteria (NTM). Current therapeutic options for these diseases are often suboptimal due to resistance to current standard of care antibiotics. A future GyrB inhibitor-based antibiotic could offer a new and effective addition to the armamentarium for treatment of mycobacterial diseases and possibly for infections caused by other bacterial pathogens. One GyrB inhibitor, SPR720, has recently completed a first-in-human clinical trial and is in clinical development for the treatment of NTM and TB infections.
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Affiliation(s)
- Suzanne S. Stokes
- Spero Therapeutics, 675 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Rajender Vemula
- Spero Therapeutics, 675 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Michael J. Pucci
- Spero Therapeutics, 675 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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10
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Li D, Liang C, Jiang Z, Zhang J, Zhuo WT, Zou FY, Wang WP, Gao GL, Song J. Visible-Light-Promoted C2 Selective Arylation of Quinoline and Pyridine N-Oxides with Diaryliodonium Tetrafluoroborate. J Org Chem 2020; 85:2733-2742. [PMID: 31906619 DOI: 10.1021/acs.joc.9b02933] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A protocol of visible-light-promoted C2 selective arylation of quinoline and pyridine N-oxides, with diaryliodonium tetrafluoroborate as an arylation reagent, using eosin Y as a photocatalyst for the construction of N-heterobiaryls was presented. This methodology provided an efficient way for the synthesis of 2-aryl-substituted quinoline and pyridine N-oxides. This strategy has the following advantages: specific regioselectivity, simple operation, good functional group tolerance, and high to moderate yields under mild conditions.
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Affiliation(s)
- Dazhi Li
- School of Life Science and Technology , Harbin Institute of Technology , Harbin , Heilongjiang 150001 , China
| | - Ce Liang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering , Harbin Institute of Technology , Harbin , Heilongjiang 150001 , China
| | - Zaixing Jiang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering , Harbin Institute of Technology , Harbin , Heilongjiang 150001 , China
| | - Junzheng Zhang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering , Harbin Institute of Technology , Harbin , Heilongjiang 150001 , China
| | - Wang-Tao Zhuo
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering , Harbin Institute of Technology , Harbin , Heilongjiang 150001 , China
| | - Fan-Yue Zou
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering , Harbin Institute of Technology , Harbin , Heilongjiang 150001 , China
| | - Wan-Peng Wang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering , Harbin Institute of Technology , Harbin , Heilongjiang 150001 , China
| | - Guo-Lin Gao
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering , Harbin Institute of Technology , Harbin , Heilongjiang 150001 , China
| | - Jinzhu Song
- School of Life Science and Technology , Harbin Institute of Technology , Harbin , Heilongjiang 150001 , China
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11
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Ismail MM, Abdulwahab HG, Nossier ES, El Menofy NG, Abdelkhalek BA. Synthesis of novel 2-aminobenzothiazole derivatives as potential antimicrobial agents with dual DNA gyrase/topoisomerase IV inhibition. Bioorg Chem 2020; 94:103437. [DOI: 10.1016/j.bioorg.2019.103437] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/28/2019] [Accepted: 11/12/2019] [Indexed: 12/31/2022]
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12
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Azam MA, Thathan J, Jupudi S. Pharmacophore modeling, atom based 3D-QSAR, molecular docking and molecular dynamics studies on Escherichia coli ParE inhibitors. Comput Biol Chem 2019; 84:107197. [PMID: 31901788 DOI: 10.1016/j.compbiolchem.2019.107197] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/20/2019] [Accepted: 12/22/2019] [Indexed: 10/25/2022]
Abstract
ATP dependent ParE enzyme is as an attractive target for the development of antibacterial agents. Atom based 3D-QSAR model AADHR.187 was developed based on the thirty eight Escherichia coli ParE inhibitors. The generated model showed statistically significant coefficient of determinations for the training (R2 = 0.985) and test (R2 = 0.86) sets. The cross-validated correlation coefficient (q2) was 0.976. The utility of the generated model was validated by the enrichment study. The model was also validated with structurally diverse external test set of ten compounds. Contour plot analysis of the generated model unveiled the chemical features necessary for the E. coli ParE enzyme inhibition. Extra-precision docking result revealed that hydrogen bonding and ionic interactions play a major role in ParE protein-ligand binding. Binding free energy was computed for the data set inhibitors to validate the binding affinity. A 30-ns molecular dynamics simulation showed high stability and effective binding of inhibitor 34 within the active site of ParE enzyme. Using the best fitted model AADHR.187, pharmacophore-based high-throughput virtual screening was performed to identify virtual hits. Based on the above studies three new molecules are proposed as E. coli ParE inhibitors with high binding affinity and favourable ADME properties.
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Affiliation(s)
- Mohammed Afzal Azam
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, Ooty, 643001, Tamil Nadu, India(1).
| | - Janarthanan Thathan
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, Ooty, 643001, Tamil Nadu, India(1)
| | - Srikanth Jupudi
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, Ooty, 643001, Tamil Nadu, India(1)
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Al-Harthy T, Zoghaib WM, Stoll R, Abdel-Jalil R. Design, synthesis, and antimicrobial evaluation of novel 2-arylbenzothiazole analogs bearing fluorine and piperazine moieties. MONATSHEFTE FUR CHEMIE 2018. [DOI: 10.1007/s00706-017-2088-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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14
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Tomašič T, Barančoková M, Zidar N, Ilaš J, Tammela P, Kikelj D. Design, synthesis, and biological evaluation of 1-ethyl-3-(thiazol-2-yl)urea derivatives as Escherichia coli
DNA gyrase inhibitors. Arch Pharm (Weinheim) 2017; 351. [DOI: 10.1002/ardp.201700333] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 11/22/2017] [Accepted: 11/24/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Tihomir Tomašič
- Faculty of Pharmacy; University of Ljubljana; Ljubljana Slovenia
| | | | - Nace Zidar
- Faculty of Pharmacy; University of Ljubljana; Ljubljana Slovenia
| | - Janez Ilaš
- Faculty of Pharmacy; University of Ljubljana; Ljubljana Slovenia
| | - Päivi Tammela
- Division of Pharmaceutical Biosciences; Faculty of Pharmacy; University of Helsinki; Helsinki Finland
| | - Danijel Kikelj
- Faculty of Pharmacy; University of Ljubljana; Ljubljana Slovenia
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15
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Azam MA, Thathan J. Pharmacophore generation, atom-based 3D-QSAR and molecular dynamics simulation analyses of pyridine-3-carboxamide-6-yl-urea analogues as potential gyrase B inhibitors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2017; 28:275-296. [PMID: 28399673 DOI: 10.1080/1062936x.2017.1310131] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 03/20/2017] [Indexed: 06/07/2023]
Abstract
DNA gyrase subunit B (GyrB) is an attractive drug target for the development of antibacterial agents with therapeutic potential. In the present study, computational studies based on pharmacophore modelling, atom-based QSAR, molecular docking, free binding energy calculation and dynamics simulation were performed on a series of pyridine-3-carboxamide-6-yl-urea derivatives. A pharmacophore model using 49 molecules revealed structural and chemical features necessary for these molecules to inhibit GyrB. The best fitted model AADDR.13 was generated with a coefficient of determination (r²) of 0.918. This model was validated using test set molecules and had a good r² of 0.78. 3D contour maps generated by the 3D atom-based QSAR revealed the key structural features responsible for the GyrB inhibitory activity. Extra precision molecular docking showed hydrogen bond interactions with key amino acid residues of ATP-binding pocket, important for inhibitor binding. Further, binding free energy was calculated by the MM-GBSA rescoring approach to validate the binding affinity. A 10 ns MD simulation of inhibitor #47 showed the stability of the predicted binding conformations. We identified 10 virtual hits by in silico high-throughput screening. A few new molecules were also designed as potent GyrB inhibitors. The information obtained from these methodologies may be helpful to design novel inhibitors of GyrB.
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Affiliation(s)
- M A Azam
- a Department of Pharmaceutical Chemistry , JSS College of Pharmacy (A Constituent College of Jagadguru Sri Sivarathreeswara University, Mysuru) , Tamil Nadu , India
| | - J Thathan
- a Department of Pharmaceutical Chemistry , JSS College of Pharmacy (A Constituent College of Jagadguru Sri Sivarathreeswara University, Mysuru) , Tamil Nadu , India
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16
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Molecular insights on analogs of imidazo[1,2-a]pyridine, azaindole, and pyridylurea towards ParE using pharmacophore modeling, molecular docking, and dynamic simulation. Struct Chem 2017. [DOI: 10.1007/s11224-017-0919-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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17
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Azam MA, Thathan J, Jubie S. Dual targeting DNA gyrase B (GyrB) and topoisomerse IV (ParE) inhibitors: A review. Bioorg Chem 2015; 62:41-63. [PMID: 26232660 DOI: 10.1016/j.bioorg.2015.07.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 07/19/2015] [Accepted: 07/20/2015] [Indexed: 01/03/2023]
Abstract
GyrB and ParE are type IIA topoisomerases and found in most bacteria. Its function is vital for DNA replication, repair and decatenation. The highly conserved ATP-binding subunits of DNA GyrB and ParE are structurally related and have been recognized as prime candidates for the development of dual-targeting antibacterial agents with broad-spectrum potential. However, no natural product or small molecule inhibitors targeting ATPase catalytic domain of both GyrB and ParE enzymes have succeeded in the clinic. Moreover, no inhibitors of these enzymes with broad-spectrum antibacterial activity against Gram-negative pathogens have been reported. Availability of high resolution crystal structures of GyrB and ParE made it possible for the design of many different classes of inhibitors with dual mechanism of action. Among them benzimidazoles, benzothiazoles, thiazolopyridines, imidiazopyridazoles, pyridines, indazoles, pyrazoles, imidazopyridines, triazolopyridines, pyrrolopyrimidines, pyrimidoindoles as well as related structures are disclosed in literatures. Unfortunately most of these inhibitors are found to be active against Gram-positive pathogens. In the present review we discuss about studies on novel dual targeting ATPase inhibitors.
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Affiliation(s)
- Mohammed Afzal Azam
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy (A Constituent College of JSS University, Mysore), Udhagamandalam 643001, Tamil Nadu, India.
| | - Janarthanan Thathan
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy (A Constituent College of JSS University, Mysore), Udhagamandalam 643001, Tamil Nadu, India
| | - Selvaraj Jubie
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy (A Constituent College of JSS University, Mysore), Udhagamandalam 643001, Tamil Nadu, India
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