1
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Sheng Q, Wang X, Hou Z, Liu B, Jiang M, Ren M, Fu J, He M, Zhang J, Xiang Y, Zhang Q, Zhou L, Deng Y, Shen X. Novel functions of o-cymen-5-ol nanoemulsion in reversing colistin resistance in multidrug-resistant Klebsiella pneumoniae infections. Biochem Pharmacol 2024; 227:116384. [PMID: 38909787 DOI: 10.1016/j.bcp.2024.116384] [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: 02/21/2024] [Revised: 06/18/2024] [Accepted: 06/20/2024] [Indexed: 06/25/2024]
Abstract
Multidrug resistance (MDR) Klebsiella pneumoniae (K. pneumoniae) is a major emerging threat to human health, and leads to very high mortality rate. The effectiveness of colistin, the last resort against MDR Gram-negative bacteria, is significantly compromised due to the widespread presence of plasmid- or chromosome-mediated resistance genes. In this study, o-cymen-5-ol has been found to greatly restore colistin sensitivity in MDR K. pneumoniae. Importantly, this compound does not impact bacterial viability, induce resistance, or cause any noticeable cell toxicity. Various routes disclosed the potential mechanism of o-cymen-5-ol potentiating colistin activity against MDR K. pneumoniae. These include inhibiting the activity of plasmid-mediated mobile colistin resistance gene (mcr-1), accelerating lipopolysaccharide (LPS) - mediated membrane damage, and promoting the ATP-binding cassette (ABC) transporter pathway. To enhance the administration and bioavailability of o-cymen-5-ol, a nanoemulsion has been designed, which significantly improves the loading efficiency and solubility of o-cymen-5-ol, resulting in antimicrobial potentiation of colistin against K. pneumoniae infection. This study has revealed a new understanding of the o-cymen-5-ol nanoemulsion as a means to enhance the effectiveness of colistin against resistant factors. The finding also suggests that o-cymen-5-ol nanoemulsion could be a promising approach in the development of potential treatments for multidrug-resistant Gram-negative bacterial infections.
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Affiliation(s)
- Qiushuang Sheng
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Xiao Wang
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Zhaoyan Hou
- Changchun Center for Disease Control and Prevention, Changchun, China
| | - Bin Liu
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Mingquan Jiang
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Mingyue Ren
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Jingchao Fu
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Miao He
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Jingchen Zhang
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Yue Xiang
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Qingbo Zhang
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Lanying Zhou
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Yanhong Deng
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China.
| | - Xue Shen
- Department of Food Science, College of Food Science and Engineering, Jilin University, Changchun 130062, China; State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China.
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2
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Gao Y, Wang H, Li X, Niu X. Molecular mechanism of green tea polyphenol epicatechin gallate attenuating Staphylococcus aureus pathogenicity by targeting Ser/Thr phosphatase Stp1. Food Funct 2023; 14:4792-4806. [PMID: 37128867 DOI: 10.1039/d3fo00170a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
In this study, through virtual screening and in vitro bioactivity assays, we discovered that (-)-epicatechin gallate (ECG), a polyphenol compound extracted from green tea, demonstrated marked anti-Ser/Thr phosphatase (Stp1) activity towards Staphylococcus aureus (S. aureus) with an IC50 value of 8.35 μM. By targeting S. aureus Stp1, ECG prevented the up-regulation of virulence gene and the formation of antibody membrane and protected the mice from S. aureus infection. Through MD simulation, the allosteric inhibitory mechanism of ECG on Stp1 was determined. The Stp1-ECG complex model underwent a significant change in conformation; its flap subdomain changed from opening to closing, whereas Stp1 activity was lost when bound to ECG. In addition, the MD simulation results of Stp1 and several tea polyphenol compounds showed that gallate groups and fewer adjacent phenolic hydroxyl groups contributed to the binding of Stp1 and inhibitors. As an inhibitor targeting S. aureus Stp1, ECG reduced the pathogenicity of S. aureus without inhibiting S. aureus, which largely reduced the possibility of drug resistance. Our findings demonstrated a novel molecular mechanism of green tea as the usual drink against S. aureus infection and elucidated the future design of allosteric inhibitors targeting Stp1.
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Affiliation(s)
- Yawen Gao
- College of Food Science and Engineering, Jilin University, Changchun 130062, P.R. China.
| | - Hongsu Wang
- College of Food Science and Engineering, Jilin University, Changchun 130062, P.R. China.
| | - Xuening Li
- College of Food Science and Engineering, Jilin University, Changchun 130062, P.R. China.
| | - Xiaodi Niu
- College of Food Science and Engineering, Jilin University, Changchun 130062, P.R. China.
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3
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Sheng Q, Hou X, Wang Y, Wang N, Deng X, Wen Z, Li D, Li L, Zhou Y, Wang J. Naringenin Microsphere as a Novel Adjuvant Reverses Colistin Resistance via Various Strategies against Multidrug-Resistant Klebsiella pneumoniae Infection. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:16201-16217. [PMID: 36530172 DOI: 10.1021/acs.jafc.2c06615] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The efficacy of colistin, the last option against multidrug-resistant (MDR) Gram-negative bacteria, is severely threatened by the prevalence of plasmid- or chromosome-mediated colistin resistance genes. Herein, naringenin has dramatically restored colistin sensitivity against colistin-resistant Klebsiella pneumoniae infection without affecting bacterial viability, inducing resistance and causing obvious cell toxicity. Mechanism analysis reveals that naringenin potentiates colistin activity by multiple strategies including inhibition of mobilized colistin resistance gene activity, repression of two-component system regulation, and acceleration of reactive oxygen species-mediated oxidative damage. A lung-targeted delivery system of naringenin microspheres has been designed to facilitate naringenin bioavailability, accompanied by an effective potentiation of colistin for Klebsiella pneumoniae infection. Consequently, a new recognition of naringenin microspheres has been elucidated to restore colistin efficacy against colistin-resistant Gram-negative pathogens, which may be an effective strategy of developing potential candidates for MDR Gram-negative bacteria infection.
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Affiliation(s)
- Qiushuang Sheng
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130012, China
| | - Xiaoning Hou
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130012, China
| | - Yang Wang
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100107, China
| | - Nan Wang
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130012, China
| | - Xuming Deng
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130012, China
| | - Zhongmei Wen
- Department of Respiratory Medicine, Center for Pathogen Biology and Infectious Diseases, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun 130021, Jilin, China
| | - Dan Li
- Department of Respiratory Medicine, Center for Pathogen Biology and Infectious Diseases, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun 130021, Jilin, China
| | - Li Li
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130012, China
| | - Yonglin Zhou
- College of Veterinary Medicine, Jilin University, Changchun 130012, China
| | - Jianfeng Wang
- Wang-College of Veterinary Medicine, Jilin University, Changchun 130012, China
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Corilagin: A Novel Antivirulence Strategy to Alleviate Streptococcus pneumoniae Infection by Diminishing Pneumolysin Oligomers. Molecules 2022; 27:molecules27165063. [PMID: 36014299 PMCID: PMC9416474 DOI: 10.3390/molecules27165063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/30/2022] [Accepted: 08/05/2022] [Indexed: 11/17/2022] Open
Abstract
Pneumolysin (PLY) is a significant virulence factor of Streptococcus pneumoniae (S. pneumoniae), able to break through the defense system of a host and mediate the occurrence of a series of infections. Therefore, PLY as the most ideal target to prevent S. pneumoniae infection has received more and more attention and research. Corilagin is a tannic acid that exhibits excellent inhibition of PLY oligomers without bacteriostatic activity to S. pneumoniae. Herein, hemolytic activity assays, cell viability tests and western blot experiments are executed to evaluate the antivirulence efficacy of corilagin against PLY in vitro. Colony observation, hematoxylin and eosin (H&E) staining and cytokines of bronchoalveolar lavage fluid (BALF) are applied to assess the therapeutic effect of corilagin in mice infected by S. pneumoniae. The results indicate the related genes of corilagin act mainly via enrichment in pathways associated with pneumonia disease. Furthermore, molecular docking and molecular dynamics simulations show that corilagin might bind with domains 3 and 4 of PLY and interfere with its hemolytic activity, which is further confirmed by the site-directed mutagenesis of PLY. Additionally, corilagin limits PLY oligomer production without impacting PLY expression in S. pneumoniae cultures. Moreover, corilagin effectively relieves PLY-mediated cell injury without any cytotoxicity, even then reducing the colony count in the lung and the levels of pro-inflammatory factors in BALF and remarkably improving lung lesions. All the results demonstrate that corilagin may be a novel strategy to cope with S. pneumoniae infection by inhibiting PLY oligomerization.
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Rios-Soto L, Téllez-Valencia A, Sierra-Campos E, Valdez-Solana M, Cisneros-Martínez J, Gómez Palacio-Gastélum M, Castillo-Villanueva A, Avitia-Domínguez C. Finding the First Potential Inhibitors of Shikimate Kinase from Methicillin Resistant Staphylococcus aureus through Computer-Assisted Drug Design. Molecules 2021; 26:molecules26216736. [PMID: 34771148 PMCID: PMC8587801 DOI: 10.3390/molecules26216736] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 11/17/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is an important threat as it causes serious hospital and community acquired infections with deathly outcomes oftentimes, therefore, development of new treatments against this bacterium is a priority. Shikimate kinase, an enzyme in the shikimate pathway, is considered a good target for developing antimicrobial drugs; this is given because of its pathway, which is essential in bacteria whereas it is absent in mammals. In this work, a computer-assisted drug design strategy was used to report the first potentials inhibitors for Shikimate kinase from methicillin-resistant Staphylococcus aureus (SaSK), employing approximately 5 million compounds from ZINC15 database. Diverse filtering criteria, related to druglike characteristics and virtual docking screening in the shikimate binding site, were performed to select structurally diverse potential inhibitors from SaSK. Molecular dynamics simulations were performed to elucidate the dynamic behavior of each SaSK–ligand complex. The potential inhibitors formed important interactions with residues that are crucial for enzyme catalysis, such as Asp37, Arg61, Gly82, and Arg138. Therefore, the compounds reported provide valuable information and can be seen as the first step toward developing SaSK inhibitors in the search of new drugs against MRSA.
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Affiliation(s)
- Lluvia Rios-Soto
- Facultad de Medicina y Nutrición, Universidad Juárez del Estado de Durango, Av. Universidad y Fanny Anitua S/N, Durango 34000, Mexico; (L.R.-S.); (J.C.-M.)
| | - Alfredo Téllez-Valencia
- Facultad de Medicina y Nutrición, Universidad Juárez del Estado de Durango, Av. Universidad y Fanny Anitua S/N, Durango 34000, Mexico; (L.R.-S.); (J.C.-M.)
- Correspondence: (A.T.-V.); (C.A.-D.); Tel./Fax: +52(618)8271382 (A.T.-V. & C.A.-D.)
| | - Erick Sierra-Campos
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Av. Artículo 123 S/N Fracc. Filadelfia, Gómez Palacio, Durango 35010, Mexico; (E.S.-C.); (M.V.-S.)
| | - Mónica Valdez-Solana
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Av. Artículo 123 S/N Fracc. Filadelfia, Gómez Palacio, Durango 35010, Mexico; (E.S.-C.); (M.V.-S.)
| | - Jorge Cisneros-Martínez
- Facultad de Medicina y Nutrición, Universidad Juárez del Estado de Durango, Av. Universidad y Fanny Anitua S/N, Durango 34000, Mexico; (L.R.-S.); (J.C.-M.)
| | - Marcelo Gómez Palacio-Gastélum
- Facultad de Odontología, Universidad Juárez del Estado de Durango, Predio Canoas S/N, Los Angeles, Durango 34070, Mexico;
| | - Adriana Castillo-Villanueva
- Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Ciudad de Mexico 04530, Mexico;
| | - Claudia Avitia-Domínguez
- Facultad de Medicina y Nutrición, Universidad Juárez del Estado de Durango, Av. Universidad y Fanny Anitua S/N, Durango 34000, Mexico; (L.R.-S.); (J.C.-M.)
- Correspondence: (A.T.-V.); (C.A.-D.); Tel./Fax: +52(618)8271382 (A.T.-V. & C.A.-D.)
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6
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Wang G, Gao Y, Xu X, Zhang P, Wang J, Li G, Lv Q, Niu X, Liu H. Mode of action and structural modelling of the interaction of formononetin with suilysin. J Appl Microbiol 2021; 131:2010-2018. [PMID: 33639036 DOI: 10.1111/jam.15051] [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: 10/28/2020] [Revised: 02/02/2021] [Accepted: 02/17/2021] [Indexed: 11/28/2022]
Abstract
AIMS Suilysin is a critical pore-forming virulence factor of Streptococcus suis that has been demonstrated to substantially contribute to its pathogenicity. We have demonstrated that formononetin alleviates S. suis infection both in vivo and in vitro by targeting suilysin. However, the molecular mechanism of the effect is unclear. Our aim was to determine the molecular mechanism of the effect of formononetin on suilysin. METHODS AND RESULTS The mechanism of interaction between formononetin and suilysin was investigated by molecular modelling. The results indicated that formononetin was bound at the junction of domain two and domain four of suilysin. The binding free energy values indicated that the A415, Y412, E414, N413, T61, T62 and G416 residues are critical for this binding, this observation was confirmed by the changes in the flexibility of these residues and the distances between these residues and formononetin. The inhibitory effect of formononetin on the pore-forming activity of suilysin, binding constant and binding free energy were significantly decreased by site-specific mutagenesis of Y412 and N413. Finally, we analysed the spatial configuration of suilysin before and after formononetin binding, the results indicated that the binding changed the conformation of suilysin, especially the angle between domain two and domain four, resulting in the disruption of cholesterol binding to suilysin and in the loss of pore-forming activity. CONCLUSIONS Formononetin is located at the junction of domain two and domain four of suilysin, and Y412 and N413 play critical roles in the binding. Formononetin binding changes the angle between domain two and domain four of suilysin, resulting in the loss of the pore-inducing activity of suilysin. SIGNIFICANCE AND IMPACT OF THE STUDY This work will promote the application of formononetin to combat S. suis infections and may contribute to the development of new inhibitors or modification of existing inhibitors.
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Affiliation(s)
- G Wang
- Department of Respiratory Medicine, the First Hospital of Jilin University, Changchun, PR China.,College of Food Engineering, Jilin Engineering Normal University, Changchun, China.,College of Veterinary Medicine, Jilin University, Changchun, China
| | - Y Gao
- Department of Respiratory Medicine, the First Hospital of Jilin University, Changchun, PR China.,College of Veterinary Medicine, Jilin University, Changchun, China
| | - X Xu
- Department of Respiratory Medicine, the First Hospital of Jilin University, Changchun, PR China.,College of Veterinary Medicine, Jilin University, Changchun, China
| | - P Zhang
- College of Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - J Wang
- Department of Respiratory Medicine, the First Hospital of Jilin University, Changchun, PR China.,College of Veterinary Medicine, Jilin University, Changchun, China
| | - G Li
- College of Veterinary Medicine, Jilin University, Changchun, China
| | - Q Lv
- Department of Respiratory Medicine, the First Hospital of Jilin University, Changchun, PR China.,College of Veterinary Medicine, Jilin University, Changchun, China
| | - X Niu
- College of Veterinary Medicine, Jilin University, Changchun, China
| | - H Liu
- Department of Respiratory Medicine, the First Hospital of Jilin University, Changchun, PR China
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7
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Wang G, Gao Y, Wu X, Gao X, Zhang M, Liu H, Fang T. Inhibitory Effect of Piceatannol on Streptococcus suis Infection Both in vitro and in vivo. Front Microbiol 2020; 11:593588. [PMID: 33329477 PMCID: PMC7728846 DOI: 10.3389/fmicb.2020.593588] [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] [Received: 08/11/2020] [Accepted: 11/04/2020] [Indexed: 11/18/2022] Open
Abstract
Suilysin (SLY) plays a critical role in Streptococcus suis infections making it an ideal target to the combat infection caused by this pathogen. In the present study, we found that piceatannol (PN), a natural compound, inhibits pore-formation by blocking the oligomerization of SLY without affecting the growth of S. suis and the expression of SLY. Furthermore, PN alleviated the J774 cell damage and the expression of the inflammatory cytokine tumor necrosis factor-α (TNF-α) and interleukin-1α (IL-1β) induced by S. suis in vitro. The computational biology and biochemistry results indicated that PN binds to the joint region of D2 and D4 in SLY, and Asn57, Pro58, Pro59, Glu76, Ile379, Glu380, and Glu418 were critical residues involved in the binding. The binding effect between PN and SLY hindered the SLY monomers from forming the oligomers, thereby weakening the hemolytic activity of SLY. This mechanism was also verified by hemolysis analysis and analysis of KA formation after site-specific mutagenesis. Furthermore, PN protected mice from S. suis infections by reducing bacterial colony formation and the inflammatory response in target organs in vivo. These results indicate that PN is a feasible drug candidate to combat S. suis infections.
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Affiliation(s)
- Guizhen Wang
- Department of Respiratory Medicine, The First Hospital of Jilin University, Jilin University, Changchun, China.,College of Food Engineering, Jilin Engineering Normal University, Changchun, China.,Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yawen Gao
- Department of Respiratory Medicine, The First Hospital of Jilin University, Jilin University, Changchun, China.,Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Xiuhua Wu
- College of Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - Xiue Gao
- College of Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - Min Zhang
- College of Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - Hongmei Liu
- Department of Respiratory Medicine, The First Hospital of Jilin University, Jilin University, Changchun, China
| | - Tianqi Fang
- Department of Respiratory Medicine, The First Hospital of Jilin University, Jilin University, Changchun, China.,Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
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Wang X, Yang Y, Gao Y, Niu X. Discovery of the Novel Inhibitor Against New Delhi Metallo-β-Lactamase Based on Virtual Screening and Molecular Modelling. Int J Mol Sci 2020; 21:ijms21103567. [PMID: 32443639 PMCID: PMC7279046 DOI: 10.3390/ijms21103567] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/07/2020] [Accepted: 05/07/2020] [Indexed: 12/20/2022] Open
Abstract
New Delhi metallo-β-lactamase (NDM-1), one of the metallo-β-lactamases (MBLs), leads to antibiotic resistance in clinical treatments due to the strong ability of hydrolysis to almost all kinds of β-lactam antibiotics. Therefore, there is the urgent need for the research and development of the novel drug-resistant inhibitors targeting NDM-1. In this study, ZINC05683641 was screened as potential NDM-1 inhibitor by virtual screening and the inhibitor mechanism of this compound was explored based on molecular dynamics simulation. The nitrocefin assay showed that the IC50 value of ZINC05683641 was 13.59 ± 0.52 μM, indicating that the hydrolytic activity of NDM-1 can be obviously suppressed by ZINC05683641. Further, the binding mode of ZINC05683641 with NDM-1 was obtained by molecular modeling, binding free energy calculation, mutagenesis assays and fluorescence-quenching assays. As results, ILE-35, MET-67, VAL-73, TRP-93, CYS-208, ASN-220 and HIS-250 played the key roles in the binding of NDM-1 with ZINC05683641. Interestingly, these key residues were exactly located in the catalytic activity region of NDM-1, implying that the inhibitor mechanism of ZINC05683641 against NDM-1 was the competitive inhibition. These findings will provide an available approach to research and develop new drug against NDM-1 and treatment for bacterial resistance.
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de Ávila MB, Bitencourt-Ferreira G, de Azevedo WF. Structural Basis for Inhibition of Enoyl-[Acyl Carrier Protein] Reductase (InhA) from Mycobacterium tuberculosis. Curr Med Chem 2020; 27:745-759. [DOI: 10.2174/0929867326666181203125229] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 07/26/2018] [Accepted: 11/14/2018] [Indexed: 12/18/2022]
Abstract
Background::
The enzyme trans-enoyl-[acyl carrier protein] reductase (InhA) is a central
protein for the development of antitubercular drugs. This enzyme is the target for the pro-drug
isoniazid, which is catalyzed by the enzyme catalase-peroxidase (KatG) to become active.
Objective::
Our goal here is to review the studies on InhA, starting with general aspects and focusing on
the recent structural studies, with emphasis on the crystallographic structures of complexes involving
InhA and inhibitors.
Method::
We start with a literature review, and then we describe recent studies on InhA crystallographic
structures. We use this structural information to depict protein-ligand interactions. We also analyze the
structural basis for inhibition of InhA. Furthermore, we describe the application of computational
methods to predict binding affinity based on the crystallographic position of the ligands.
Results::
Analysis of the structures in complex with inhibitors revealed the critical residues responsible
for the specificity against InhA. Most of the intermolecular interactions involve the hydrophobic residues
with two exceptions, the residues Ser 94 and Tyr 158. Examination of the interactions has shown
that many of the key residues for inhibitor binding were found in mutations of the InhA gene in the
isoniazid-resistant Mycobacterium tuberculosis. Computational prediction of the binding affinity for
InhA has indicated a moderate uphill relationship with experimental values.
Conclusion::
Analysis of the structures involving InhA inhibitors shows that small modifications on
these molecules could modulate their inhibition, which may be used to design novel antitubercular
drugs specific for multidrug-resistant strains.
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Affiliation(s)
- Maurício Boff de Ávila
- Laboratory of Computational Systems Biology, School of Sciences - Pontifical Catholic University of Rio, Grande do Sul (PUCRS), Av. Ipiranga, 6681, Porto Alegre-RS 90619-900, Brazil
| | - Gabriela Bitencourt-Ferreira
- Laboratory of Computational Systems Biology, School of Sciences - Pontifical Catholic University of Rio, Grande do Sul (PUCRS), Av. Ipiranga, 6681, Porto Alegre-RS 90619-900, Brazil
| | - Walter Filgueira de Azevedo
- Laboratory of Computational Systems Biology, School of Sciences - Pontifical Catholic University of Rio, Grande do Sul (PUCRS), Av. Ipiranga, 6681, Porto Alegre-RS 90619-900, Brazil
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Targeting staphylocoagulase with isoquercitrin protects mice from Staphylococcus aureus-induced pneumonia. Appl Microbiol Biotechnol 2020; 104:3909-3919. [PMID: 32130467 DOI: 10.1007/s00253-020-10486-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/10/2020] [Accepted: 02/18/2020] [Indexed: 10/24/2022]
Abstract
Staphylocoagulase (Coa) is a virulence factor of Staphylococcus aureus (S. aureus) that promotes blood coagulation by activating prothrombin to convert fibrinogen to fibrin. Coa plays a crucial role in disease pathogenesis and is a promising target for the treatment of S. aureus infections. Here, we identified that isoquercitrin, a natural flavonol compound, can markedly reduce the activity of Coa at concentrations that have no effect on bacterial growth. Mechanistic studies employing molecular dynamics simulation revealed that isoquercitrin binds to Coa by interacting with Asp-181 and Tyr-188, thereby affecting the binding of Coa to prothrombin. Importantly, in vivo studies showed that isoquercitrin treatment significantly reduced the bacterial burden, pathological damage, and inflammation of lung tissue and improved the percentage of survival of mice infected with S. aureus Newman strain. These data suggest that isoquercitrin is a promising inhibitor of Coa that can be used for the development of therapeutic drugs to combat S. aureus infections.Key Points• Staphylocoagulase plays a key role in the pathogenesis of S. aureus infection.• We identified that isoquercitrin is a direct inhibitor of staphylocoagulase.• Isoquercitrin treatment can significantly attenuate S. aureus virulence in vivo.
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Design, synthesis and biological evaluation of 5-(2-(4-(substituted benzo[d]isoxazol-3-yl)piperazin-1-yl)acetyl)indolin-2-one and 5-(2-(4-substitutedpiperazin-1-yl)acetyl)indolin-2-one analogues as novel anti-tubercular agents. ARAB J CHEM 2019. [DOI: 10.1016/j.arabjc.2015.02.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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12
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Teng Z, Guo Y, Liu X, Zhang J, Niu X, Yu Q, Deng X, Wang J. Theaflavin-3,3´-digallate increases the antibacterial activity of β-lactam antibiotics by inhibiting metallo-β-lactamase activity. J Cell Mol Med 2019; 23:6955-6964. [PMID: 31392792 PMCID: PMC6787515 DOI: 10.1111/jcmm.14580] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/27/2019] [Accepted: 07/11/2019] [Indexed: 01/16/2023] Open
Abstract
Metallo-β-lactamases (MBLs) are some of the best known β-lactamases produced by common Gram-positive and Gram-negative pathogens and are crucial factors in the rise of bacterial resistance against β-lactam antibiotics. Although many types of β-lactamase inhibitors have been successfully developed and used in clinical settings, no MBL inhibitors have been identified to date. Nitrocefin, checkerboard and time-kill assays were used to examine the enzyme behaviour in vitro. Molecular docking calculation, molecular dynamics simulation, calculation of the binding free energy and ligand-residue interaction decomposition were used for mechanistic research. The behaviour of the enzymes in vivo was investigated by a mouse infection experiment. We showed that theaflavin-3,3´-digallate (TFDG), a natural compound lacking antibacterial activities, can inhibit the hydrolysis of MBLs. In the checkerboard and time-kill assays, we observed a synergistic effect of TFDG with β-lactam antibiotics against methicillin-resistant Staphylococcus aureus BAA1717. Molecular dynamics simulations were used to identify the mechanism of the inhibition of MBLs by TFDG, and we observed that the hydrolysis activity of the MBLs was restricted by the binding of TFDG to Gln242 and Ser369. Furthermore, the combination of TFDG with β-lactam antibiotics showed effective protection in a mouse Staphylococcus aureus pneumonia model. These findings suggest that TFDG can effectively inhibit the hydrolysis activity of MBLs and enhance the antibacterial activity of β-lactam antibiotics against pathogens in vitro and in vivo.
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Affiliation(s)
- Zihao Teng
- Department of Respiratory MedicineThe First Hospital of Jilin UniversityChangchunChina
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary MedicineJilin UniversityChangchunChina
| | - Yan Guo
- Department of Respiratory MedicineThe First Hospital of Jilin UniversityChangchunChina
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary MedicineJilin UniversityChangchunChina
| | - Xingqi Liu
- Department of Respiratory MedicineThe First Hospital of Jilin UniversityChangchunChina
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary MedicineJilin UniversityChangchunChina
| | - Jian Zhang
- Department of Respiratory MedicineThe First Hospital of Jilin UniversityChangchunChina
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary MedicineJilin UniversityChangchunChina
| | - Xiaodi Niu
- Department of Respiratory MedicineThe First Hospital of Jilin UniversityChangchunChina
| | - Qinlei Yu
- Jilin Provincial Animal Disease Control CenterChangchunChina
| | - Xuming Deng
- Department of Respiratory MedicineThe First Hospital of Jilin UniversityChangchunChina
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary MedicineJilin UniversityChangchunChina
| | - Jianfeng Wang
- Department of Respiratory MedicineThe First Hospital of Jilin UniversityChangchunChina
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary MedicineJilin UniversityChangchunChina
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Tarabini RF, Timmers LFSM, Sequeiros-Borja CE, Norberto de Souza O. The importance of the quaternary structure to represent conformational ensembles of the major Mycobacterium tuberculosis drug target. Sci Rep 2019; 9:13683. [PMID: 31548581 PMCID: PMC6757107 DOI: 10.1038/s41598-019-50213-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 09/03/2019] [Indexed: 12/29/2022] Open
Abstract
Flexibility is a feature intimately related to protein function, since conformational changes can be used to describe environmental changes, chemical modifications, protein-protein and protein-ligand interactions. In this study, we have investigated the influence of the quaternary structure of 2-trans-enoyl-ACP (CoA) reductase or InhA, from Mycobacterium tuberculosis, to its flexibility. We carried out classical molecular dynamics simulations using monomeric and tetrameric forms to elucidate the enzyme's flexibility. Overall, we observed statistically significant differences between conformational ensembles of tertiary and quaternary structures. In addition, the enzyme's binding site is the most affected region, reinforcing the importance of the quaternary structure to evaluate the binding affinity of small molecules, as well as the effect of single point mutations to InhA protein dynamics.
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Affiliation(s)
- Renata Fioravanti Tarabini
- Laboratório de Bioinformática, Modelagem e Simulação de Biossistemas (LABIO), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Av. Ipiranga 6681, 90619-900, Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, PUCRS, Porto Alegre, RS, Brazil
| | - Luís Fernando Saraiva Macedo Timmers
- Laboratório de Bioinformática, Modelagem e Simulação de Biossistemas (LABIO), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Av. Ipiranga 6681, 90619-900, Porto Alegre, RS, Brazil. .,Programa de Pós-Graduação em Biologia Celular e Molecular, PUCRS, Porto Alegre, RS, Brazil. .,Programa de Pós-Graduação em Biotecnologia (PPGBiotec), Universidade do Vale do Taquari -Univates, Rua Avelino Talini, 171 - Bairro Universitário, Lajeado, RS, Brazil.
| | - Carlos Eduardo Sequeiros-Borja
- Laboratório de Bioinformática, Modelagem e Simulação de Biossistemas (LABIO), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Av. Ipiranga 6681, 90619-900, Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, PUCRS, Porto Alegre, RS, Brazil.,Faculty of Biology, Institute of Molecular Biology and Biotechnology, Department of Gene Expression, Laboratory of Biomolecular Interactions and Transport, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Osmar Norberto de Souza
- Laboratório de Bioinformática, Modelagem e Simulação de Biossistemas (LABIO), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Av. Ipiranga 6681, 90619-900, Porto Alegre, RS, Brazil. .,Programa de Pós-Graduação em Biologia Celular e Molecular, PUCRS, Porto Alegre, RS, Brazil.
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14
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Wang L, Li B, Si X, Liu X, Deng X, Niu X, Jin Y, Wang D, Wang J. Quercetin protects rats from catheter-related Staphylococcus aureus infections by inhibiting coagulase activity. J Cell Mol Med 2019; 23:4808-4818. [PMID: 31094081 PMCID: PMC6584481 DOI: 10.1111/jcmm.14371] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 03/18/2019] [Accepted: 04/22/2019] [Indexed: 11/30/2022] Open
Abstract
Coagulase (Coa) activity is essential for the virulence of Staphylococcus aureus (S aureus), one of the most important pathogenic bacteria leading to catheter‐related bloodstream infections (CRBSI). We have demonstrated that the mutation of coagulase improved outcomes in disease models of S aureus CRBSI, suggesting that targeting Coa may represent a novel antiinfective strategy for CRBSI. Here, we found that quercetin, a natural compound that does not affect S aureus viability, could inhibit Coa activity. Chemical biological analysis revealed that the direct engagement of quercetin with the active site (residues Tyr187, Leu221 and His228) of Coa inhibited its activity. Furthermore, treatment with quercetin reduced the retention of bacteria on catheter surfaces, decreased the bacterial load in the kidneys and alleviated kidney abscesses in vivo. These data suggest that antiinfective therapy targeting Coa with quercetin may represent a novel strategy and provide a new leading compound with which to combat bacterial infections.
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Affiliation(s)
- Lin Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, Jilin, China
| | - BangBang Li
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, Jilin, China.,College of Animal Science, Jilin University, Changchun, Jilin, China.,The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xiaosa Si
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, Jilin, China
| | - Xingyuan Liu
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, Jilin, China
| | - Xuming Deng
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, Jilin, China
| | - Xiaodi Niu
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, Jilin, China
| | - Yingli Jin
- Department of Pharmacology, College of Basic Medical Science, Jilin University, Changchun, Jilin, China
| | - Dacheng Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, Jilin, China.,College of Animal Science, Jilin University, Changchun, Jilin, China
| | - Jianfeng Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, Jilin, China
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15
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Yu Y, Wang X, Gao Y, Yang Y, Sun L, Wang G, Deng X, Niu X. Molecular modeling and QM/MM calculation clarify the catalytic mechanism of β-lactamase N1. J Mol Model 2019; 25:118. [PMID: 30982150 DOI: 10.1007/s00894-019-4001-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 03/21/2019] [Indexed: 11/28/2022]
Abstract
The treatment of bacterial infections is currently threatened by the emergence of pathogenic bacteria producing β-lactamase, which catalyzes the hydrolysis of β-lactams. Although the hydrolysis of the substrate nitrocefin by a metallo-β-lactamase, namely β-lactamase N1 from USA300 (a typical methicillin-resistant Staphylococcus aureus), has previously been reported in the literature, its mechanism remains elusive. Here, we show that molecular modeling and quantum-mechanical/molecular mechanics (QM/MM) calculations describing the complex of β-lactamase N1 with nitrocefin (the substrate of β-lactamase N1) can predict the catalytic mechanism of nitrocefin hydrolysis by β-lactamase N1. Molecular dynamics simulation shows that the catalytic reaction begins with hydrogen bond formation between Gln171 and a water molecule, which is thereby captured for nitrocefin hydrolysis by β-lactamase N1. In addition, the carboxyl group coordinates Zn2 in a chelating fashion. The binding energy decompositions suggest that Phe169 anchors nitrocefin by π-stacking interactions between the benzene rings. Specifically, Phe169 and Zn2 position the nitrocefin in specific orientations. The active site of β-lactamase N1 contains two residues (Gln171 and Phe169) that we expected to be crucial for guiding the nitrocefin hydrolysis reaction. Compelling evidence is provided that the mutants F169A and Q171A show lower enzymatic activity than the wild-type protein. On the basis of the QM/MM calculations, we propose that nitrocefin hydrolysis is initiated by the interaction between the oxygen atom of water and the C18 atom of nitrocefin, leading to the opening of the four-membered ring of nitrocefin and the formation of a substrate intermediate. In the next step, a hydrogen atom transfers from the nitrogen atom to the C11 atom of nitrocefin, resulting in the stable product.
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Affiliation(s)
- Yiding Yu
- Department of Food Quality and Safety, Jilin University, Xi'an Road 5333, Changchun, 130062, China
| | - Xiyan Wang
- Department of Food Quality and Safety, Jilin University, Xi'an Road 5333, Changchun, 130062, China
| | - Yawen Gao
- Department of Food Quality and Safety, Jilin University, Xi'an Road 5333, Changchun, 130062, China
| | - Yanan Yang
- Department of Food Quality and Safety, Jilin University, Xi'an Road 5333, Changchun, 130062, China
| | - Lin Sun
- Department of Food Quality and Safety, Jilin University, Xi'an Road 5333, Changchun, 130062, China
| | - Guizhen Wang
- Department of Food Quality and Safety, Jilin University, Xi'an Road 5333, Changchun, 130062, China
| | - Xuming Deng
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333, Changchun, 130062, China.
| | - Xiaodi Niu
- Department of Food Quality and Safety, Jilin University, Xi'an Road 5333, Changchun, 130062, China.
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16
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Bezzina B, Djémil R, Khatmi DE, Humbel S, Carissan Y. Computational insights about the dynamic behavior for the inclusion process of deprotonated and neutral aspirin in β-cyclodextrin. J INCL PHENOM MACRO 2018. [DOI: 10.1007/s10847-018-0822-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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17
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Structural characterization, biochemical, inhibition and computational studies of Entamoeba histolytica phosphoglycerate mutase: finding hits for a new antiamoebic drug. Med Chem Res 2018. [DOI: 10.1007/s00044-018-2184-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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18
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Campaniço A, Moreira R, Lopes F. Drug discovery in tuberculosis. New drug targets and antimycobacterial agents. Eur J Med Chem 2018; 150:525-545. [DOI: 10.1016/j.ejmech.2018.03.020] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 03/05/2018] [Accepted: 03/06/2018] [Indexed: 01/24/2023]
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19
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Niu X, Yu Y, Guo H, Yang Y, Wang G, Sun L, Gao Y, Yu Z, Wang H. Molecular modeling reveals the inhibition mechanism and binding mode of ursolic acid to TLR4-MD2. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2017.11.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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20
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Vázquez-Raygoza A, Cano-González L, Velázquez-Martínez I, Trejo-Soto PJ, Castillo R, Hernández-Campos A, Hernández-Luis F, Oria-Hernández J, Castillo-Villanueva A, Avitia-Domínguez C, Sierra-Campos E, Valdez-Solana M, Téllez-Valencia A. Species-Specific Inactivation of Triosephosphate Isomerase from Trypanosoma brucei: Kinetic and Molecular Dynamics Studies. Molecules 2017; 22:molecules22122055. [PMID: 29186784 PMCID: PMC6149853 DOI: 10.3390/molecules22122055] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 11/19/2017] [Accepted: 11/21/2017] [Indexed: 01/07/2023] Open
Abstract
Human African Trypanosomiasis (HAT), a disease that provokes 2184 new cases a year in Sub-Saharan Africa, is caused by Trypanosoma brucei. Current treatments are limited, highly toxic, and parasite strains resistant to them are emerging. Therefore, there is an urgency to find new drugs against HAT. In this context, T. brucei depends on glycolysis as the unique source for ATP supply; therefore, the enzyme triosephosphate isomerase (TIM) is an attractive target for drug design. In the present work, three new benzimidazole derivatives were found as TbTIM inactivators (compounds 1, 2 and 3) with an I50 value of 84, 82 and 73 µM, respectively. Kinetic analyses indicated that the three molecules were selective when tested against human TIM (HsTIM) activity. Additionally, to study their binding mode in TbTIM, we performed a 100 ns molecular dynamics simulation of TbTIM-inactivator complexes. Simulations showed that the binding of compounds disturbs the structure of the protein, affecting the conformations of important domains such as loop 6 and loop 8. In addition, the physicochemical and drug-like parameters showed by the three compounds suggest a good oral absorption. In conclusion, these molecules will serve as a guide to design more potent inactivators that could be used to obtain new drugs against HAT.
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Affiliation(s)
- Alejandra Vázquez-Raygoza
- Faculty of Medicine and Nutrition, Juarez University of Durango State, Av. Universidad y Fanny Anitua S/N, Durango 34000, Mexico; (A.V.-R.); (C.A.-D.)
| | - Lucia Cano-González
- School of Chemistry, Pharmacy Department, National Autonomous University of Mexico, Mexico City 04510, Mexico; (L.C.-G.); (I.V.-M.); (P.J.T.-S.); (R.C.); (A.H.-C.); (F.H.-L.)
| | - Israel Velázquez-Martínez
- School of Chemistry, Pharmacy Department, National Autonomous University of Mexico, Mexico City 04510, Mexico; (L.C.-G.); (I.V.-M.); (P.J.T.-S.); (R.C.); (A.H.-C.); (F.H.-L.)
| | - Pedro Josué Trejo-Soto
- School of Chemistry, Pharmacy Department, National Autonomous University of Mexico, Mexico City 04510, Mexico; (L.C.-G.); (I.V.-M.); (P.J.T.-S.); (R.C.); (A.H.-C.); (F.H.-L.)
| | - Rafael Castillo
- School of Chemistry, Pharmacy Department, National Autonomous University of Mexico, Mexico City 04510, Mexico; (L.C.-G.); (I.V.-M.); (P.J.T.-S.); (R.C.); (A.H.-C.); (F.H.-L.)
| | - Alicia Hernández-Campos
- School of Chemistry, Pharmacy Department, National Autonomous University of Mexico, Mexico City 04510, Mexico; (L.C.-G.); (I.V.-M.); (P.J.T.-S.); (R.C.); (A.H.-C.); (F.H.-L.)
| | - Francisco Hernández-Luis
- School of Chemistry, Pharmacy Department, National Autonomous University of Mexico, Mexico City 04510, Mexico; (L.C.-G.); (I.V.-M.); (P.J.T.-S.); (R.C.); (A.H.-C.); (F.H.-L.)
| | - Jesús Oria-Hernández
- Biochemistry and Genetics Laboratory, National Institute of Pediatrics, Ministry of Health, Mexico City 04534, Mexico; (J.O.-H.); (A.C.-V.)
| | - Adriana Castillo-Villanueva
- Biochemistry and Genetics Laboratory, National Institute of Pediatrics, Ministry of Health, Mexico City 04534, Mexico; (J.O.-H.); (A.C.-V.)
| | - Claudia Avitia-Domínguez
- Faculty of Medicine and Nutrition, Juarez University of Durango State, Av. Universidad y Fanny Anitua S/N, Durango 34000, Mexico; (A.V.-R.); (C.A.-D.)
| | - Erick Sierra-Campos
- Faculty of Chemical Sciences, Juarez University of Durango State, Av. Artículo 123 S/N Fracc. Filadelfia, Gomez Palacio, Durango 35010, Mexico; (E.S.-C.); (M.V.-S)
| | - Mónica Valdez-Solana
- Faculty of Chemical Sciences, Juarez University of Durango State, Av. Artículo 123 S/N Fracc. Filadelfia, Gomez Palacio, Durango 35010, Mexico; (E.S.-C.); (M.V.-S)
| | - Alfredo Téllez-Valencia
- Faculty of Medicine and Nutrition, Juarez University of Durango State, Av. Universidad y Fanny Anitua S/N, Durango 34000, Mexico; (A.V.-R.); (C.A.-D.)
- Correspondence: ; Tel./Fax: +52-618-812-1687
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Synthesis and pharmacological evaluation of pyridinyl-1,3,4-oxadiazolyl-ethanone derivatives as antimicrobial, antifungal and antitubercular agents. Med Chem Res 2017. [DOI: 10.1007/s00044-017-2098-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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22
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Fekri R, Salehi M, Asadi A, Kubicki M. Spectroscopic studies, structural characterization and electrochemical studies of two cobalt (III) complexes with tridentate hydrazone Schiff base ligands: Evaluation of antibacterial activities, DNA‐binding, BSA interaction and molecular docking. Appl Organomet Chem 2017. [DOI: 10.1002/aoc.4019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Roghayeh Fekri
- Department of Chemistry, College of ScienceSemnan University Semnan Iran
| | - Mehdi Salehi
- Department of Chemistry, College of ScienceSemnan University Semnan Iran
| | - Asadollah Asadi
- Department of Biology, Faculty of ScienceUniversity of Mohaghegh Ardabili Ardabil Iran
| | - Maciej Kubicki
- Faculty of ChemistryAdam Mickiewicz University Umultowska 89b 61‐614 Poznan Poland
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23
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24
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Fekri R, Salehi M, Asadi A, Kubicki M. DNA/BSA interaction, bio-activity, molecular docking simulation study and electrochemical properties of hydrazone Schiff base derived Cu(II)/Ni(II) metal complexes: Influence of the nuclearity and metal ions. Polyhedron 2017. [DOI: 10.1016/j.poly.2017.02.047] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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25
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Inturi B, Pujar GV, Purohit MN. Recent Advances and Structural Features of Enoyl-ACP Reductase Inhibitors of Mycobacterium tuberculosis. Arch Pharm (Weinheim) 2016; 349:817-826. [PMID: 27775177 DOI: 10.1002/ardp.201600186] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 10/05/2016] [Accepted: 10/06/2016] [Indexed: 12/31/2022]
Abstract
Mycobacterium tuberculosis enoyl-ACP reductase (InhA) has been validated as a promising target for antitubercular agents. Isoniazid (INH), the most prescribed drug to treat tuberculosis (TB), inhibits a NADH-dependent InhA that provides precursors of mycolic acids, which are components of the mycobacterial cell wall. It is a pro-drug that needs activation to form the inhibitory INH-NAD adduct by KatG coding for catalase-peroxidase. The INH resistance of M. tuberculosis is caused by mutations in KatG, which may lead to multidrug-resistant TB (MDR-TB). Hence, there is a need for new drugs that can combat MDR-TB. The rationale for the development of new drugs to combat MDR-TB strains is the design of InhA inhibitors that can bypass bioactivation by KatG. In the present review, special attention was paid to discuss the chemical nature and recent developments of direct InhA inhibitors. The InhA inhibitors reported here have significant inhibitory effects against Mtb InhA. The diphenyl ether derivatives have shown slow onset, a tight-binding mechanism, and high affinity at the InhA active site. However, some of the diphenyl ethers have significant in vitro efficacy, which fails to transform into in vivo efficacy. Among the InhA inhibitors, 4-hydroxy-2-pyridones have emerged as a new chemical class with significant InhA inhibitory activity and better pharmacokinetic parameters when compared to diphenyl ethers.
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Affiliation(s)
- Bharathkumar Inturi
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, Jagadguru Sri Shivarathreeshwara University, Mysore, Karnataka, India
| | - Gurubasavaraj V Pujar
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, Jagadguru Sri Shivarathreeshwara University, Mysore, Karnataka, India.
| | - Madhusudhan N Purohit
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, Jagadguru Sri Shivarathreeshwara University, Mysore, Karnataka, India
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26
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Wang J, Zhou X, Li W, Deng X, Deng Y, Niu X. Curcumin protects mice from Staphylococcus aureus pneumonia by interfering with the self-assembly process of α-hemolysin. Sci Rep 2016; 6:28254. [PMID: 27345357 PMCID: PMC4921848 DOI: 10.1038/srep28254] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 06/01/2016] [Indexed: 02/07/2023] Open
Abstract
α-hemolysin (Hla) is a self-assembling extracellular protein secreted as a soluble monomer by most Staphylococcus aureus strains and is an essential virulence factor for the pathogenesis of various S. aureus infections. Here, we show that curcumin (CUR), a natural compound with weak anti-S. aureus activity, can inhibit the hemolysis induced by Hla. Molecular dynamics simulations, free energy calculations, and mutagenesis assays were further employed for the Hla-CUR complex to determine the mechanism of such inhibition. The analysis of this combined approach indicated that the direct binding CUR to Hla blocks the conformational transition of Hla from the monomer to the oligomer, leading to an inhibition of Hla hemolytic activity. We also found that the addition of CUR significantly attenuated Hla-mediated injury of human alveolar cell (A549) co-cultured with S. aureus. The in vivo data further demonstrated that treatment with CUR protects mice from pneumonia caused by S. aureus, including methicillin-resistant strains (MRSA). These findings suggest that CUR inhibits the pore-forming activity of Hla through a novel mechanism, which would pave the way for the development of new and more effective antibacterial agents to combat S. aureus pneumonia.
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Affiliation(s)
- Jianfeng Wang
- Key Laboratory of Zoonosis, Ministry of Education, Institute of Zoonosis, and Department of Food Quality and Safety, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Xuan Zhou
- Key Laboratory of Zoonosis, Ministry of Education, Institute of Zoonosis, and Department of Food Quality and Safety, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Wenhua Li
- Key Laboratory of Zoonosis, Ministry of Education, Institute of Zoonosis, and Department of Food Quality and Safety, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Xuming Deng
- Key Laboratory of Zoonosis, Ministry of Education, Institute of Zoonosis, and Department of Food Quality and Safety, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yanhong Deng
- Key Laboratory of Zoonosis, Ministry of Education, Institute of Zoonosis, and Department of Food Quality and Safety, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Xiaodi Niu
- Key Laboratory of Zoonosis, Ministry of Education, Institute of Zoonosis, and Department of Food Quality and Safety, College of Veterinary Medicine, Jilin University, Changchun, China
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27
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Kumar V, Sobhia ME. Molecular dynamics-based investigation of InhA substrate binding loop for diverse biological activity of direct InhA inhibitors. J Biomol Struct Dyn 2016; 34:2434-52. [DOI: 10.1080/07391102.2015.1118410] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Vivek Kumar
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar 160 062, Punjab, India
| | - M. Elizabeth Sobhia
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar 160 062, Punjab, India
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Wang L, Bi C, Cai H, Liu B, Zhong X, Deng X, Wang T, Xiang H, Niu X, Wang D. The therapeutic effect of chlorogenic acid against Staphylococcus aureus infection through sortase A inhibition. Front Microbiol 2015; 6:1031. [PMID: 26528244 PMCID: PMC4608362 DOI: 10.3389/fmicb.2015.01031] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 09/11/2015] [Indexed: 12/17/2022] Open
Abstract
The emergence and wide spread of multi-drug resistant Staphylococcus aureus (S. aureus) requires the development of new therapeutic agents with alternative modes of action. Anti-virulence strategies are hoped to meet that need. Sortase A (SrtA) has attracted great interest as a potential drug target to treat infections caused by S. aureus, as many of the surface proteins displayed by SrtA function as virulence factors by mediating bacterial adhesion to specific organ tissues, invasion of host cells, and evasion of the host-immune responses. It has been suggested that inhibitors of SrtA might be promising candidates for the treatment and/or prevention of S. aureus infections. In this study, we report that chlorogenic acid (CHA), a natural compound that lacks significant anti-S. aureus activity, inhibit the activity of SrtA in vitro (IC50 = 33.86 ± 5.55 μg/ml) and the binding of S. aureus to fibrinogen (Fg). Using molecular dynamics simulations and mutagenesis assays, we further demonstrate that CHA binds to the binding sites of C184 and G192 in the SrtA. In vivo studies demonstrated that CHA prevent mice from S. aureus-induced renal abscess, resulting in a significant survival advantage. These findings indicate that CHA is a promising therapeutic compound against SrtA during S. aureus infections.
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Affiliation(s)
- Lin Wang
- Key Laboratory of Zoonosis Research, Ministry of Education/Institute of Zoonosis/College of Veterinary Medicine, Jilin University Changchun, China
| | - Chongwei Bi
- College of Animal Science, Jilin University Changchun, China
| | - Hongjun Cai
- The College of Animal Science and Technology, Jilin Agricultural University Changchun, China
| | - Bingrun Liu
- College of Animal Science, Jilin University Changchun, China
| | - Xiaobo Zhong
- College of Animal Science, Jilin University Changchun, China
| | - Xuming Deng
- Key Laboratory of Zoonosis Research, Ministry of Education/Institute of Zoonosis/College of Veterinary Medicine, Jilin University Changchun, China
| | - Tiedong Wang
- College of Animal Science, Jilin University Changchun, China
| | - Hua Xiang
- The College of Animal Science and Technology, Jilin Agricultural University Changchun, China
| | - Xiaodi Niu
- Key Laboratory of Zoonosis Research, Ministry of Education/Department of Food Quality and Safety/College of Veterinary Medicine, Jilin University Changchun, China
| | - Dacheng Wang
- College of Animal Science, Jilin University Changchun, China
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Rajkhowa S, Jha AN, Deka RC. Anti-tubercular drug development: computational strategies to identify potential compounds. J Mol Graph Model 2015; 62:56-68. [PMID: 26386453 DOI: 10.1016/j.jmgm.2015.09.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 08/13/2015] [Accepted: 09/05/2015] [Indexed: 10/23/2022]
Abstract
InhA is an attractive target to combat tuberculosis (TB), which is targeted by many pro-drugs (isoniazid, etc.) and drugs such as triclosan. However, triclosan is less useful as an antitubercular drug due to its low bioavailability and therefore, in order to overcome this difficulty, many derivatives of triclosan were prepared. Here, we have combined various computational techniques to virtually screen out four potential triclosan derivatives. Molecular docking methods have been employed to screen out 32 out of 62 triclosan derivatives considering the mode of binding and the top re-rank scores. A comparative study on the chemical properties of triclosan and some of its derivatives has been performed using density functional theory (DFT) calculations. DFT based global reactivity descriptors (GRD), such as hardness, chemical potential, chemical softness, electrophilicity index, Fukui function, and local philicity calculated at the optimized geometries were used to investigate the usefulness of these descriptors for understanding the reactive nature and sites of the molecules. QSAR equations were built using these descriptors considering these 32 compounds. Four common compounds showing the best correlation and the best docking scores were considered for the ADMET property calculations and their dynamical movements have been studied using molecular dynamics simulations. Our results showed that these four compounds are chemically more active than triclosan and have the potential to inhibit the Mycobacterium tuberculosis enoyl acyl carrier protein reductase. This work shows that combination of different computational techniques may help to screen out potential drug candidates from a list of possible ones.
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Affiliation(s)
- Sanchaita Rajkhowa
- Department of Chemical Sciences, Tezpur University, Napaam, Tezpur 784028, Assam, India
| | - Anupam Nath Jha
- Department of Molecular Biology & Biotechnology, Tezpur University, Napaam, Tezpur 784028, Assam, India
| | - Ramesh Chandra Deka
- Department of Chemical Sciences, Tezpur University, Napaam, Tezpur 784028, Assam, India.
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Novel inhibitor discovery and the conformational analysis of inhibitors of listeriolysin O via protein-ligand modeling. Sci Rep 2015; 5:8864. [PMID: 25749652 PMCID: PMC4352855 DOI: 10.1038/srep08864] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 02/06/2015] [Indexed: 12/04/2022] Open
Abstract
Increasing bacterial resistance to available antibiotics makes the discovery of novel efficacious antibacterial agents a priority. A previous report showed that listeriolysin O (LLO) is a critical virulence factor and suggested that it is a target for developing anti-virulence drugs against Listeria monocytogenes infections. In this study, we report the discovery of LLO natural compound inhibitors with differential activity by using hemolysis assay. The mechanism of action of the inhibitors was consistent with that of fisetin, a natural flavonoid without antimicrobial activity, which we showed in our previous report via molecular simulation. Furthermore, a substantial increase in anti-hemolytic activity was observed when the single bond (C1-C2) was replaced by a double bond (C1-C2) in the inhibitor molecule. This change was based on the decomposition of the ligand-residue interaction, which indicated that the double bond (C1-C2) in the inhibitors was required for their inhibition of LLO. The current MD simulation work provides insights into the mechanism by which the compounds inhibit LLO at the atomic level and will be useful for the development of new, selective LLO inhibitors.
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Naidu KM, Nagesh HN, Singh M, Sriram D, Yogeeswari P, Gowri Chandra Sekhar KV. Novel amide and sulphonamide derivatives of 6-(piperazin-1-yl)phenanthridine as potent Mycobacterium tuberculosis H37Rv inhibitors. Eur J Med Chem 2015; 92:415-26. [PMID: 25590862 DOI: 10.1016/j.ejmech.2015.01.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 11/22/2014] [Accepted: 01/08/2015] [Indexed: 11/25/2022]
Abstract
A series of thirty three novel 6-(piperazin-1-yl)phenanthridine amide and sulphonamide analogues were synthesized, characterized and screened for their in vitro antimycobacterial activity against Mycobacterium tuberculosis (MTB) H37Rv strain. These compounds exhibited minimum inhibitory concentration (MIC) between 1.56 and ≥50 μg/mL. Out of these derivatives, few compounds 6l, 6r, 7b, 7f, 7g and 7k exhibited moderate activity (MIC = 6.25 μg/mL) and compounds 6b, 6e, 6k, 6n, 7h, 7i and 7n displayed good activity (MIC = 3.13 μg/mL), whereas compounds 6m, 6s and 7d exhibited excellent anti-tubercular activity (MIC = 1.56 μg/mL). In addition, MTT assay was accomplished on the active analogues of the series against mouse macrophage (RAW 264.7) cells to evaluate the toxicity profile of the newly synthesized compounds and selectivity index of the compounds was determined. Additionally, compounds 6b and 7d were docked to the ATPase domain of M. tuberculosis GyrB protein to know the interaction profile and structures of compounds 6b and 7d were further substantiated through single crystal XRD.
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Affiliation(s)
- Kalaga Mahalakshmi Naidu
- Department of Chemistry, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Jawahar Nagar, Shamirpet Mandal, Hyderabad 500 078, Telangana, India
| | - Hunsur Nagendra Nagesh
- Department of Chemistry, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Jawahar Nagar, Shamirpet Mandal, Hyderabad 500 078, Telangana, India
| | - Manjeet Singh
- Department of Chemistry, Banaras Hindu University, Varanasi 221 005, India
| | - Dharmarajan Sriram
- Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Jawahar Nagar, Shamirpet Mandal, Hyderabad 500 078, Telangana, India
| | - Perumal Yogeeswari
- Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Jawahar Nagar, Shamirpet Mandal, Hyderabad 500 078, Telangana, India
| | - Kondapalli Venkata Gowri Chandra Sekhar
- Department of Chemistry, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Jawahar Nagar, Shamirpet Mandal, Hyderabad 500 078, Telangana, India.
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Duan X, Xiang X, Xie J. Crucial components of mycobacterium type II fatty acid biosynthesis (Fas-II) and their inhibitors. FEMS Microbiol Lett 2014; 360:87-99. [DOI: 10.1111/1574-6968.12597] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 09/09/2014] [Accepted: 09/11/2014] [Indexed: 01/27/2023] Open
Affiliation(s)
- Xiangke Duan
- Institute of Modern Biopharmaceuticals; State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area; Key Laboratory of Eco-Environments in Three Gorges Reservoir Region; Ministry of Education; School of Life Sciences; Southwest University; Beibei Chongqing China
| | - Xiaohong Xiang
- Institute of Modern Biopharmaceuticals; State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area; Key Laboratory of Eco-Environments in Three Gorges Reservoir Region; Ministry of Education; School of Life Sciences; Southwest University; Beibei Chongqing China
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals; State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area; Key Laboratory of Eco-Environments in Three Gorges Reservoir Region; Ministry of Education; School of Life Sciences; Southwest University; Beibei Chongqing China
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Wang J, Qiu J, Tan W, Zhang Y, Wang H, Zhou X, Liu S, Feng H, Li W, Niu X, Deng X. Fisetin inhibits Listeria monocytogenes virulence by interfering with the oligomerization of listeriolysin O. J Infect Dis 2014; 211:1376-87. [PMID: 25231018 DOI: 10.1093/infdis/jiu520] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 08/04/2014] [Indexed: 11/14/2022] Open
Abstract
Listeriolysin O (LLO), an essential virulence determinant of Listeria monocytogenes, is a pore-forming toxin whose primary function is to facilitate cytosolic bacterial replication by breaching the phagosomal membranes, which is critical for the pathogen to evade host immune recognition. The critical role of LLO in the virulence of L. monocytogenes renders it an ideal target for designing novel antivirulence therapeutics. We found that fisetin, a natural flavonoid without antimicrobial activity, is a potent antagonist of LLO-mediated hemolysis. Fisetin effectively inhibits L. monocytogenes infection in both tissue culture and animal infection models. Molecular modeling and mutational analysis revealed that fisetin directly engages loop 2 and loop 3 of LLO, leading to the blockage of cholesterol binding and the reduction of its oligomerization, thus inhibiting its hemolytic activity. Our results establish fisetin as an effective antitoxin agent for LLO, which can be further developed into novel therapeutics against infections caused by L. monocytogenes.
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Affiliation(s)
- Jianfeng Wang
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine
| | - Jiazhang Qiu
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine
| | - Wei Tan
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine
| | - Yu Zhang
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine
| | - Hongshu Wang
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine
| | - Xuan Zhou
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine
| | - Shui Liu
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine
| | - Haihua Feng
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine
| | - Wenhua Li
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine
| | - Xiaodi Niu
- Department of Food Quality and Safety, Jilin University, Changchun, China
| | - Xuming Deng
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine
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Elucidating the structural basis of diphenyl ether derivatives as highly potent enoyl-ACP reductase inhibitors through molecular dynamics simulations and 3D-QSAR study. J Mol Model 2014; 20:2319. [PMID: 24935113 DOI: 10.1007/s00894-014-2319-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 05/26/2014] [Indexed: 10/25/2022]
Abstract
Diphenyl ether derivatives are good candidates for anti-tuberculosis agents that display a promising potency for inhibition of InhA, an essential enoyl-acyl carrier protein (ACP) reductase involved in fatty acid biosynthesis pathways in Mycobacterium tuberculosis. In this work, key structural features for the inhibition were identified by 3D-QSAR CoMSIA models, constructed based on available experimental binding properties of diphenyl ether inhibitors, and a set of four representative compounds was subjected to MD simulations of inhibitor-InhA complexes for the calculation of binding free energies. The results show that bulky groups are required for the R1 substituent on the phenyl A ring of the inhibitors to favor a hydrophobic pocket formed by residues Phe149, Met155, Pro156, Ala157, Tyr158, Pro193, Met199, Val203, Leu207, Ile215, and Leu218. Small substituents with a hydrophilic property are required at the R3 and R4 positions of the inhibitor phenyl B rings to form hydrogen bonds with the backbones of Gly96 and Met98, respectively. For the R2 substituent, small substituents with simultaneous hydrophilic or hydrophobic properties are required to favor the interaction with the pyrophosphate moiety of NAD(+) and the methyl side chain of Ala198, respectively. The reported data provide structural guidance for the design of new and potent diphenyl ether-based inhibitors with high inhibitory activities against M. tuberculosis InhA.
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35
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Deng F, Ma S, Xie M, Zhang X, Li P, Zhai H. Study on the agonists for the human Toll-like receptor-8 by molecular modeling. MOLECULAR BIOSYSTEMS 2014; 10:2202-14. [DOI: 10.1039/c4mb00183d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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36
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Martins F, Santos S, Ventura C, Elvas-Leitão R, Santos L, Vitorino S, Reis M, Miranda V, Correia HF, Aires-de-Sousa J, Kovalishyn V, Latino DA, Ramos J, Viveiros M. Design, synthesis and biological evaluation of novel isoniazid derivatives with potent antitubercular activity. Eur J Med Chem 2014; 81:119-38. [DOI: 10.1016/j.ejmech.2014.04.077] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 03/08/2014] [Accepted: 04/26/2014] [Indexed: 11/28/2022]
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Bello M, Mendieta-Wejebe JE, Correa-Basurto J. Structural and energetic analysis to provide insight residues of CYP2C9, 2C11 and 2E1 involved in valproic acid dehydrogenation selectivity. Biochem Pharmacol 2014; 90:145-58. [PMID: 24794636 DOI: 10.1016/j.bcp.2014.04.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 04/23/2014] [Accepted: 04/25/2014] [Indexed: 11/17/2022]
Abstract
Docking and molecular dynamics (MD) simulation have been two computational techniques used to gain insight about the substrate orientation within protein active sites, allowing to identify potential residues involved in the binding and catalytic mechanisms. In this study, both methods were combined to predict the regioselectivity in the binding mode of valproic acid (VPA) on three cytochrome P-450 (CYP) isoforms CYP2C9, CYP2C11, and CYP2E1, which are involved in the biotransformation of VPA yielding reactive hepatotoxic intermediate 2-n-propyl-4-pentenoic acid (4nVPA). There are experimental data about hydrogen atom abstraction of the C4-position of VPA to yield 4nVPA, however, there are not structural evidence about the binding mode of VPA and 4nVPA on CYPs. Therefore, the complexes between these CYP isoforms and VPA or 4nVPA were studied to explore their differences in binding and energetic stabilization. Docking results showed that VPA and 4nVPA are coupled into CYPs binding site in a similar conformation, but it does not explain the VPA hydrogen atom abstraction. On the other hand, MD simulations showed a set of energetic states that reorient VPA at the first ns, then making it susceptible to a dehydrogenation reaction. For 4nVPA, multiple binding modes were observed in which the different states could favor either undergo other reaction mechanism or ligand expulsion from the binding site. Otherwise, the energetic and entropic contribution point out a similar behavior for the three CYP complexes, showing as expected a more energetically favorable binding free energy for the complexes between CYPs and VPA than with 4nVPA.
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Affiliation(s)
- Martiniano Bello
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos de la Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Casco de Santo Tomás, México, Distrito Federal 11340, Mexico.
| | - Jessica E Mendieta-Wejebe
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos de la Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Casco de Santo Tomás, México, Distrito Federal 11340, Mexico
| | - José Correa-Basurto
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos de la Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Casco de Santo Tomás, México, Distrito Federal 11340, Mexico.
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Towards the identification of the binding site of benzimidazoles to β-tubulin of Trichinella spiralis: Insights from computational and experimental data. J Mol Graph Model 2013; 41:12-9. [DOI: 10.1016/j.jmgm.2013.01.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 01/26/2013] [Accepted: 01/29/2013] [Indexed: 11/24/2022]
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39
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Niu X, Wang X, Wang H, Gao X, Wang Y, Wang S. Insights into the specific binding site of adenosine to the Stx2, the protein toxin fromEscherichia coliO157:H7 using molecular dynamics simulations and free energy calculations. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2012.713483] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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40
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Dong J, Qiu J, Zhang Y, Lu C, Dai X, Wang J, Li H, Wang X, Tan W, Luo M, Niu X, Deng X. Oroxylin A inhibits hemolysis via hindering the self-assembly of α-hemolysin heptameric transmembrane pore. PLoS Comput Biol 2013; 9:e1002869. [PMID: 23349625 PMCID: PMC3547825 DOI: 10.1371/journal.pcbi.1002869] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 11/16/2012] [Indexed: 02/06/2023] Open
Abstract
Alpha-hemolysin (α-HL) is a self-assembling, channel-forming toxin produced by most Staphylococcus aureus strains as a 33.2-kDa soluble monomer. Upon binding to a susceptible cell membrane, the monomer self-assembles to form a 232.4-kDa heptamer that ultimately causes host cell lysis and death. Consequently, α-HL plays a significant role in the pathogenesis of S. aureus infections, such as pneumonia, mastitis, keratitis and arthritis. In this paper, experimental studies show that oroxylin A (ORO), a natural compound without anti-S. aureus activity, can inhibit the hemolytic activity of α-HL. Molecular dynamics simulations, free energy calculations, and mutagenesis assays were performed to understand the formation of the α-HL-ORO complex. This combined approach revealed that the catalytic mechanism of inhibition involves the direct binding of ORO to α-HL, which blocks the conformational transition of the critical “Loop” region of the α-HL protein thereby inhibiting its hemolytic activity. This mechanism was confirmed by experimental data obtained from a deoxycholate-induced oligomerization assay. It was also found that, in a co-culture system with S. aureus and human alveolar epithelial (A549) cells, ORO could protect against α-HL-mediated injury. These findings indicate that ORO hinders the lytic activity of α-HL through a novel mechanism, which should facilitate the design of new and more effective antibacterial agents against S. aureus. The mechanism controlling protein-ligand interactions is one of the most important processes in rational drug design. X-ray crystallography is a traditional tool used to investigate the interaction of ligands and proteins in a complex. However, protein crystallography is inefficient, and the development of crystal technology and research remains unequally distributed. Thus, it seems impractical to explore the structure of the α-hemolysin-ORO monomer complex by crystallography. Therefore, we used molecular dynamics simulations to investigate the receptor-ligand interaction in the α-HL-ORO monomer complex. In this study, we found that oroxylin A (ORO), a natural compound with little anti-S. aureus activity, can inhibit the hemolytic activity of α-HL at low concentrations. Through molecular docking and molecular dynamics simulations, we determined the potential binding mode of the protein-ligand interaction. The data revealed that ORO directly binds to α-HL, an interaction that blacks the conformational transition of the critical “Loop” region in α-HL and thus prevents the formation of the α-HL heptameric transmembrane pore, which ultimately inhibits the hemolytic activity of α-HL. This mechanism was confirmed by experimental data. Furthermore, we demonstrated that ORO could protect against α-HL-mediated injury in human alveolar epithelial (A549) cells.
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Affiliation(s)
- Jing Dong
- Key Laboratory of Zoonosis, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
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Niu X, Qiu J, Wang X, Gao X, Dong J, Wang J, Li H, Zhang Y, Dai X, Lu C, Deng X. Molecular insight into the inhibition mechanism of cyrtominetin to α-hemolysin by molecular dynamics simulation. Eur J Med Chem 2013; 62:320-8. [PMID: 23376250 DOI: 10.1016/j.ejmech.2013.01.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 01/04/2013] [Accepted: 01/08/2013] [Indexed: 11/16/2022]
Abstract
The protein α-hemolysin (α-HL) is a self-assembling exotoxin that binds to the membrane of a susceptible host cell. In this paper, experimental studies show that cyrtominetin (CTM) can inhibit the hemolytic activity of α-HL. To understand how CTM can affect hemolytic activity, molecular dynamics simulations were carried out for α-HL-CTM complex and these results were compared with the crystal structure of monomeric α-HL. With this approach, the analysis revealed that the inhibition of CTM involves CTM directly binding to α-HL. Due to the binding of CTM, the conformation of the critical "Loop" region was restrained. This mechanism was confirmed by the experimental data. These findings indicate that CTM hinders the lysis activity of α-HL through a novel mechanism.
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Affiliation(s)
- Xiaodi Niu
- Department of Food Quality and Safety, Jilin University, Changchun 130062, China
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Niu X, Gao X, Wang H, Wang X, Wang S. Insight into the dynamic interaction between different flavonoids and bovine serum albumin using molecular dynamics simulations and free energy calculations. J Mol Model 2012; 19:1039-47. [PMID: 23114430 DOI: 10.1007/s00894-012-1649-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Accepted: 10/14/2012] [Indexed: 11/24/2022]
Abstract
In this study, the binding of Bovine serum albumin (BSA) with three flavonoids, kaempferol-3-O-a-L-rhamnopyranosyl-(1-3)-a-L-rhamnopyranosyl-(1-6)-b-D-galacto- pyranoside (drug 1),kaempfol-7-O-rhamnosyl-3-O-rutinoside (drug 2)andkaempferide-7-O-(4"-O-acetylrhamnosyl)-3-O-ruti- noside (drug 3) is investigated by molecular docking, molecular dynamics (MD) simulation, and binding free energy calculation. The free energies are consistent with available experimental results and suggest that the binding site of BSA-drug1 is more stable than those of BSA-drug2 and BSA-drug3. The energy decomposition analysis is performed and reveals that the electrostatic interactions play an important role in the stabilization of the binding site of BSA-drug1 while the van der Waals interactions contribute largely to stabilization of the binding site of BSA-drug2 and BSA-drug3. The key residues stabilizing the binding sites of BSA-drug1, BSA-drug2 and BSA-drug3 are identified based on the residue decomposition analysis.
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Affiliation(s)
- Xiaodi Niu
- Department of Food quality and Safety, Jilin University, Changchun 130062, People's Republic of China.
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Poschlad A, Meded V, Maul R, Wenzel W. Different interface orientations of pentacene and PTCDA induce different degrees of disorder. NANOSCALE RESEARCH LETTERS 2012; 7:248. [PMID: 22583772 PMCID: PMC3479028 DOI: 10.1186/1556-276x-7-248] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Accepted: 04/17/2012] [Indexed: 05/31/2023]
Abstract
: Organic polymers or crystals are commonly used in manufacturing of today's electronically functional devices (OLEDs, organic solar cells, etc). Understanding their morphology in general and at the interface in particular is of paramount importance. Proper knowledge of molecular orientation at interfaces is essential for predicting optoelectronic properties such as exciton diffusion length, charge carrier mobility, and molecular quadrupole moments. Two promising candidates are pentacene and 3,4:9,10-perylenetetracarboxylic dianhydride (PTCDA). Different orientations of pentacene on PTCDA have been investigated using an atomistic molecular dynamics approach. Here, we show that the degree of disorder at the interface depends largely on the crystal orientation and that more ordered interfaces generally suffer from large vacancy formation.
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Affiliation(s)
- Angela Poschlad
- Steinbuch Centre for Computing, Karlsruhe Institute of Technology (KIT), Karlsruhe, 76131, Germany
- Institute for Nanotechnology, Karlsruhe Institute of Technology (KIT), Karlsruhe, 76131, Germany
| | - Velimir Meded
- Steinbuch Centre for Computing, Karlsruhe Institute of Technology (KIT), Karlsruhe, 76131, Germany
- Institute for Nanotechnology, Karlsruhe Institute of Technology (KIT), Karlsruhe, 76131, Germany
| | - Robert Maul
- Steinbuch Centre for Computing, Karlsruhe Institute of Technology (KIT), Karlsruhe, 76131, Germany
| | - Wolfgang Wenzel
- Institute for Nanotechnology, Karlsruhe Institute of Technology (KIT), Karlsruhe, 76131, Germany
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Qiu J, Niu X, Dong J, Wang D, Wang J, Li H, Luo M, Li S, Feng H, Deng X. Baicalin Protects Mice From Staphylococcus aureus Pneumonia Via Inhibition of the Cytolytic Activity of α-Hemolysin. J Infect Dis 2012; 206:292-301. [DOI: 10.1093/infdis/jis336] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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