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Onyenaka C, Idowu KA, Ha NP, Graviss EA, Olaleye OA. Anti-Tuberculosis Potential of OJT008 against Active and Multi-Drug-Resistant Mycobacterium Tuberculosis: In Silico and In Vitro Inhibition of Methionine Aminopeptidase. Int J Mol Sci 2023; 24:17142. [PMID: 38138972 PMCID: PMC10742973 DOI: 10.3390/ijms242417142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/22/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
Despite the recent progress in the diagnosis of tuberculosis (TB), the chemotherapeutic management of TB continues to be challenging. Mycobacterium tuberculosis (Mtb), the etiological agent of TB, is classified as the 13th leading cause of death globally. In addition, 450,000 people were reported to develop multi-drug-resistant TB globally. The current project focuses on targeting methionine aminopeptidase (MetAP), an essential protein for the viability of Mtb. MetAP is a metalloprotease that catalyzes the excision of the N-terminal methionine (NME) during protein synthesis, allowing the enzyme to be an auspicious target for the development of novel therapeutic agents for the treatment of TB. Mtb possesses two MetAP1 isoforms, MtMetAP1a and MtMetAP1c, which are vital for Mtb viability and, hence, a promising chemotherapeutic target for Mtb therapy. In this study, we cloned and overexpressed recombinant MtMetAP1c. We investigated the in vitro inhibitory effect of the novel MetAP inhibitor, OJT008, on the cobalt ion- and nickel ion-activated MtMetAP1c, and the mechanism of action was elucidated through an in silico approach. The compound's potency against replicating and multi-drug-resistant (MDR) Mtb strains was also investigated. The induction of the overexpressed recombinant MtMetAP1c was optimized at 8 h with a final concentration of 1 mM Isopropyl β-D-1-thiogalactopyranoside. The average yield from 1 L of Escherichia coli culture for MtMetAP1c was 4.65 mg. A preliminary MtMetAP1c metal dependency screen showed optimum activation with nickel and cobalt ions occurred at 100 µM. The half-maximal inhibitory concentration (IC50) values of OJT008 against MtMetAP1c activated with CoCl2 and NiCl2 were 11 µM and 40 µM, respectively. The in silico study showed OJT008 strongly binds to both metal-activated MtMetAP1c, as evidenced by strong molecular interactions and a higher binding score, thereby corroborating our result. This in silico study validated the pharmacophore's metal specificity. The potency of OJT008 against both active and MDR Mtb was <0.063 µg/mL. Our study reports OJT008 as an inhibitor of MtMetAP1c, which is potent at low micromolar concentrations against both active susceptible and MDR Mtb. These results suggest OJT008 is a potential lead compound for the development of novel small molecules for the therapeutic management of TB.
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Affiliation(s)
- Collins Onyenaka
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX 77004, USA (K.A.I.)
| | - Kehinde A. Idowu
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX 77004, USA (K.A.I.)
| | - Ngan P. Ha
- Center for Infectious Disease Research, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Edward A. Graviss
- Center for Infectious Disease Research, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Omonike A. Olaleye
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX 77004, USA (K.A.I.)
- Center for Infectious Disease Research, Houston Methodist Research Institute, Houston, TX 77030, USA
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Vasile S, Roos K. Understanding the Structure-Activity Relationship through Density Functional Theory: A Simple Method Predicts Relative Binding Free Energies of Metalloenzyme Fragment-like Inhibitors. ACS OMEGA 2023; 8:21438-21449. [PMID: 37360476 PMCID: PMC10285960 DOI: 10.1021/acsomega.2c08156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 03/29/2023] [Indexed: 06/28/2023]
Abstract
Despite being involved in several human diseases, metalloenzymes are targeted by a small percentage of FDA-approved drugs. Development of novel and efficient inhibitors is required, as the chemical space of metal binding groups (MBGs) is currently limited to four main classes. The use of computational chemistry methods in drug discovery has gained momentum thanks to accurate estimates of binding modes and binding free energies of ligands to receptors. However, exact predictions of binding free energies in metalloenzymes are challenging due to the occurrence of nonclassical phenomena and interactions that common force field-based methods are unable to correctly describe. In this regard, we applied density functional theory (DFT) to predict the binding free energies and to understand the structure-activity relationship of metalloenzyme fragment-like inhibitors. We tested this method on a set of small-molecule inhibitors with different electronic properties and coordinating two Mn2+ ions in the binding site of the influenza RNA polymerase PAN endonuclease. We modeled the binding site using only atoms from the first coordination shell, hence reducing the computational cost. Thanks to the explicit treatment of electrons by DFT, we highlighted the main contributions to the binding free energies and the electronic features differentiating strong and weak inhibitors, achieving good qualitative correlation with the experimentally determined affinities. By introducing automated docking, we explored alternative ways to coordinate the metal centers and we identified 70% of the highest affinity inhibitors. This methodology provides a fast and predictive tool for the identification of key features of metalloenzyme MBGs, which can be useful for the design of new and efficient drugs targeting these ubiquitous proteins.
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Hoff CC, Azevedo MF, Thurler AB, Maluf SEC, Melo PMS, del Rivero MA, González-Bacerio J, Carmona AK, Budu A, Gazarini ML. Overexpression of Plasmodium falciparum M1 Aminopeptidase Promotes an Increase in Intracellular Proteolysis and Modifies the Asexual Erythrocytic Cycle Development. Pathogens 2021; 10:pathogens10111452. [PMID: 34832608 PMCID: PMC8618464 DOI: 10.3390/pathogens10111452] [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: 09/11/2021] [Revised: 11/05/2021] [Accepted: 11/06/2021] [Indexed: 11/16/2022] Open
Abstract
Plasmodium falciparum, the most virulent of the human malaria parasite, is responsible for high mortality rates worldwide. We studied the M1 alanyl-aminopeptidase of this protozoan (PfA-M1), which is involved in the final stages of hemoglobin cleavage, an essential process for parasite survival. Aiming to help in the rational development of drugs against this target, we developed a new strain of P. falciparum overexpressing PfA-M1 without the signal peptide (overPfA-M1). The overPfA-M1 parasites showed a 2.5-fold increase in proteolytic activity toward the fluorogenic substrate alanyl-7-amido-4-methylcoumarin, in relation to the wild-type group. Inhibition studies showed that overPfA-M1 presented a lower sensitivity against the metalloaminopeptidase inhibitor bestatin and to other recombinant PfA-M1 inhibitors, in comparison with the wild-type strain, indicating that PfA-M1 is a target for the in vitro antimalarial activity of these compounds. Moreover, overPfA-M1 parasites present a decreased in vitro growth, showing a reduced number of merozoites per schizont, and also a decrease in the iRBC area occupied by the parasite in trophozoite and schizont forms when compared to the controls. Interestingly, the transgenic parasite displays an increase in the aminopeptidase activity toward Met-, Ala-, Leu- and Arg-7-amido-4-methylcoumarin. We also investigated the potential role of calmodulin and cysteine proteases in PfA-M1 activity. Taken together, our data show that the overexpression of PfA-M1 in the parasite cytosol can be a suitable tool for the screening of antimalarials in specific high-throughput assays and may be used for the identification of intracellular molecular partners that modulate their activity in P. falciparum.
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Affiliation(s)
- Carolina C. Hoff
- Department of Biosciences, Federal University of São Paulo, Santos 11015-020, Brazil; (C.C.H.); (M.F.A.)
| | - Mauro F. Azevedo
- Department of Biosciences, Federal University of São Paulo, Santos 11015-020, Brazil; (C.C.H.); (M.F.A.)
| | - Adriana B. Thurler
- Department of Biophysics, Federal University of São Paulo, São Paulo 04039-032, Brazil; (A.B.T.); (S.E.C.M.); (P.M.S.M.); (A.K.C.)
| | - Sarah El Chamy Maluf
- Department of Biophysics, Federal University of São Paulo, São Paulo 04039-032, Brazil; (A.B.T.); (S.E.C.M.); (P.M.S.M.); (A.K.C.)
| | - Pollyana M. S. Melo
- Department of Biophysics, Federal University of São Paulo, São Paulo 04039-032, Brazil; (A.B.T.); (S.E.C.M.); (P.M.S.M.); (A.K.C.)
| | - Maday Alonso del Rivero
- Center for Protein Studies, Faculty of Biology, University of Havana, Vedado, La Habana 10400, Cuba; (M.A.d.R.); (J.G.-B.)
| | - Jorge González-Bacerio
- Center for Protein Studies, Faculty of Biology, University of Havana, Vedado, La Habana 10400, Cuba; (M.A.d.R.); (J.G.-B.)
| | - Adriana K. Carmona
- Department of Biophysics, Federal University of São Paulo, São Paulo 04039-032, Brazil; (A.B.T.); (S.E.C.M.); (P.M.S.M.); (A.K.C.)
| | - Alexandre Budu
- Department of Biophysics, Federal University of São Paulo, São Paulo 04039-032, Brazil; (A.B.T.); (S.E.C.M.); (P.M.S.M.); (A.K.C.)
- Correspondence: (A.B.); (M.L.G.)
| | - Marcos L. Gazarini
- Department of Biosciences, Federal University of São Paulo, Santos 11015-020, Brazil; (C.C.H.); (M.F.A.)
- Correspondence: (A.B.); (M.L.G.)
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Mishra R, Chaurasia H, Singh VK, Naaz F, Singh RK. Molecular modeling, QSAR analysis and antimicrobial properties of Schiff base derivatives of isatin. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130763] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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5
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Boucherit H, Chikhi A, Bensegueni A, Merzoug A, Bolla JM. The Research of New Inhibitors of Bacterial Methionine Aminopeptidase by Structure Based Virtual Screening Approach of ZINC DATABASE and In Vitro Validation. Curr Comput Aided Drug Des 2021; 16:389-401. [PMID: 31244429 DOI: 10.2174/1573409915666190617165643] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 04/26/2019] [Accepted: 05/06/2019] [Indexed: 01/13/2023]
Abstract
BACKGROUND The great emergence of multi-resistant bacterial strains and the low renewal of antibiotics molecules are leading human and veterinary medicine to certain therapeutic impasses. Therefore, there is an urgent need to find new therapeutic alternatives including new molecules in the current treatments of infectious diseases. Methionine aminopeptidase (MetAP) is a promising target for developing new antibiotics because it is essential for bacterial survival. OBJECTIVE To screen for potential MetAP inhibitors by in silico virtual screening of the ZINC database and evaluate the best potential lead molecules by in vitro studies. METHODS We have considered 200,000 compounds from the ZINC database for virtual screening with FlexX software to identify potential inhibitors against bacterial MetAP. Nine chemical compounds of the top hits predicted were purchased and evaluated in vitro. The antimicrobial activity of each inhibitor of MetAP was tested by the disc-diffusion assay against one Gram-positive (Staphylococcus aureus) and two Gram-negative (Escherichia coli & Pseudomonas aeruginosa) bacteria. Among the studied compounds, compounds ZINC04785369 and ZINC03307916 showed promising antibacterial activity. To further characterize their efficacy, the minimum inhibitory concentration was determined for each compound by the microdilution method which showed significant results. RESULTS These results suggest compounds ZINC04785369 and ZINC03307916 as promising molecules for developing MetAP inhibitors. CONCLUSION Furthermore, they could therefore serve as lead molecules for further chemical modifications to obtain clinically useful antibacterial agents.
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Affiliation(s)
- Hanane Boucherit
- Laboratory of Applied Biochemistry, Department of Biochemistry and Cellular and Molecular Biology, Faculty of Natural and Life Sciences, Mentouri Brothers University, Constantine 1, Algeria
| | - Abdelouahab Chikhi
- Laboratory of Applied Biochemistry, Department of Biochemistry and Cellular and Molecular Biology, Faculty of Natural and Life Sciences, Mentouri Brothers University, Constantine 1, Algeria
| | - Abderrahmane Bensegueni
- Laboratory of Applied Biochemistry, Department of Biochemistry and Cellular and Molecular Biology, Faculty of Natural and Life Sciences, Mentouri Brothers University, Constantine 1, Algeria
| | - Amina Merzoug
- Laboratory of Applied Biochemistry, Department of Biochemistry and Cellular and Molecular Biology, Faculty of Natural and Life Sciences, Mentouri Brothers University, Constantine 1, Algeria
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6
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Quan DH, Nagalingam G, Luck I, Proschogo N, Pillalamarri V, Addlagatta A, Martinez E, Sintchenko V, Rutledge PJ, Triccas JA. Bengamides display potent activity against drug-resistant Mycobacterium tuberculosis. Sci Rep 2019; 9:14396. [PMID: 31591407 PMCID: PMC6779907 DOI: 10.1038/s41598-019-50748-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 09/18/2019] [Indexed: 01/08/2023] Open
Abstract
Mycobacterium tuberculosis infects over 10 million people annually and kills more people each year than any other human pathogen. The current tuberculosis (TB) vaccine is only partially effective in preventing infection, while current TB treatment is problematic in terms of length, complexity and patient compliance. There is an urgent need for new drugs to combat the burden of TB disease and the natural environment has re-emerged as a rich source of bioactive molecules for development of lead compounds. In this study, one species of marine sponge from the Tedania genus was found to yield samples with exceptionally potent activity against M. tuberculosis. Bioassay-guided fractionation identified bengamide B as the active component, which displayed activity in the nanomolar range against both drug-sensitive and drug-resistant M. tuberculosis. The active compound inhibited in vitro activity of M. tuberculosis MetAP1c protein, suggesting the potent inhibitory action may be due to interference with methionine aminopeptidase activity. Tedania-derived bengamide B was non-toxic against human cell lines, synergised with rifampicin for in vitro inhibition of bacterial growth and reduced intracellular replication of M. tuberculosis. Thus, bengamides isolated from Tedania sp. show significant potential as a new class of compounds for the treatment of drug-resistant M. tuberculosis.
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Affiliation(s)
- Diana H Quan
- Discipline of Infectious Diseases and Immunology, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia.,Tuberculosis Research Program, Centenary Institute, Sydney, NSW, Australia
| | - Gayathri Nagalingam
- Discipline of Infectious Diseases and Immunology, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia.,Tuberculosis Research Program, Centenary Institute, Sydney, NSW, Australia
| | - Ian Luck
- School of Chemistry, Faculty of Science, The University of Sydney, Camperdown, NSW, Australia
| | - Nicholas Proschogo
- School of Chemistry, Faculty of Science, The University of Sydney, Camperdown, NSW, Australia
| | | | - Anthony Addlagatta
- Centre for Chemical Biology, Indian Institute of Chemical Technology, Secunderabad, India
| | - Elena Martinez
- Centre for Infectious Diseases and Microbiology, The Westmead Institute, Westmead, NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Camperdown, NSW, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology, The Westmead Institute, Westmead, NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Camperdown, NSW, Australia
| | - Peter J Rutledge
- School of Chemistry, Faculty of Science, The University of Sydney, Camperdown, NSW, Australia
| | - James A Triccas
- Discipline of Infectious Diseases and Immunology, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia. .,Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia. .,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Camperdown, NSW, Australia.
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7
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Hasan P, Pillalamarri VK, Aneja B, Irfan M, Azam M, Perwez A, Maguire R, Yadava U, Kavanagh K, Daniliuc CG, Ahmad MB, Rizvi MMA, Rizwanul Haq QM, Addlagatta A, Abid M. Synthesis and mechanistic studies of diketo acids and their bioisosteres as potential antibacterial agents. Eur J Med Chem 2018; 163:67-82. [PMID: 30503944 DOI: 10.1016/j.ejmech.2018.11.053] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 10/13/2018] [Accepted: 11/21/2018] [Indexed: 11/16/2022]
Abstract
A series of diketo esters and their pertinent bioisosteres were designed and synthesized as potent antibacterial agents by targeting methionine amino peptidases (MetAPs). In the biochemical assay against purified MetAPs from Streptococcus pneumoniae (SpMetAP1a), Mycobacterium tuberculosis (MtMetAP1c), Enterococcus faecalis (EfMetAP1a) and human (HsMetAP1b), compounds 3a, 4a and 5a showed more than 85% inhibition of all the tested MetAPs at 100 μM concentration. Compounds 4a and 5a also exhibited antibacterial potential with MIC values 62.5 μg/mL (S. pneumoniae), 31.25 μg/mL (E. faecalis), 62.5 μg/mL (Escherichia coli) and 62.5 μg/mL (S. pneumoniae), 62.5 μg/mL (E. coli), respectively. Moreover, 5a also significantly inhibited the growth of multidrug resistant E. coli strains at 512 μg/mL conc., while showing no cytotoxic effect towards healthy CHO cells and thus being selected. Growth kinetics study showed significant inhibition of bacterial growth when treated with different conc. of 5a. TEM analysis also displayed vital damage to bacterial cells by 5a at MIC conc. Moreover, significant inhibition of biofilm formation was observed in bacterial cells treated with MIC conc. of 5a as visualized by SEM micrographs. Interestingly, 5a did not cause an alteration in the hemocyte density in Galleria mellonella larvae which is considered in vivo model for antimicrobial studies and was non-toxic up to a conc. of 2.5 mg/mL.
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Affiliation(s)
- Phool Hasan
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India; Department of Chemistry, TNB College, TM Bhagalpur University, Bhagalpur, 812007, India
| | - Vijay K Pillalamarri
- Centre for Chemical Biology, Indian Institute of Chemical Technology, Tarnaka, Hyderabad, 500607, India
| | - Babita Aneja
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Mohammad Irfan
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Mudsser Azam
- Microbiology Research Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Ahmad Perwez
- Genome Biology Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Ronan Maguire
- Department of Biology, Maynooth University, Co. Kildare, W23 F2H6, Ireland
| | - Umesh Yadava
- Department of Physics, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, Uttar Pradesh, 273009, India
| | - Kevin Kavanagh
- Department of Biology, Maynooth University, Co. Kildare, W23 F2H6, Ireland
| | | | - Md Belal Ahmad
- Department of Chemistry, TNB College, TM Bhagalpur University, Bhagalpur, 812007, India
| | - M Moshahid A Rizvi
- Genome Biology Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Qazi Mohd Rizwanul Haq
- Microbiology Research Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Anthony Addlagatta
- Centre for Chemical Biology, Indian Institute of Chemical Technology, Tarnaka, Hyderabad, 500607, India
| | - Mohammad Abid
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India.
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8
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Synthesis, docking, ADMET prediction, cytotoxicity and antimicrobial activity of oxathiadiazole derivatives. Comput Biol Chem 2018; 77:226-239. [PMID: 30366286 DOI: 10.1016/j.compbiolchem.2018.10.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 09/29/2018] [Accepted: 10/10/2018] [Indexed: 11/23/2022]
Abstract
A series of molecules bearing oxathiadiazole, a five membered heterocyclic ring has been designed, synthesized and screened for antimicrobial activity. Molecules, 1a, 1b, 1d, 3a-b and 4a-b were found to be highly active (MIC value upto 1.5 μg/mL) against different human pathogens, namely S. aureus, B. cerus, P. aeruginosa and E. coli. Some of the compounds, 1a, 1b and 1d have also shown the antifungal activity (MIC value upto 6.2 μg/mL) against Candida albicans, Candida glubrate and Candida crusei. During in vitro cytotoxicity study, the oxathiadiazole derivatives showed less toxicity than the reference used against PBM, CEM and Vero (African green monkey kidney) cell lines. Docking studies suggested that all designed ligands interacted well within active site of PDF enzyme (PDB ID: 1G2A). Oxathiadiazole ring of all ligands formed H-bond with amino acid Leu91 at a distance ranging between 2.5-2.8 Å and also exhibited π - + and π - π interactions with amino acid residues Arg97 and His132, respectively. In silico ADMET evaluations of compounds showed more than 90% intestinal absorption for all compounds except 4b (87.45%), which too was greater than the reference drugs sulfamethoxazole (76.46%) and chloramphenicol (69.94%). TOPKAT results also supported the lower cytotoxicity of all compounds.
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Qiu WW, Xu J, Li JY, Li J, Nan FJ. Activity-based protein profiling for type I methionine aminopeptidase by using photo-affinity trimodular probes. Chembiochem 2016; 8:1351-8. [PMID: 17623306 DOI: 10.1002/cbic.200700148] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Wen-Wei Qiu
- Chinese National Center for Drug Screening, Shanghai Institute of Materia Medica, 189 Guo Shou Jing Road, Shanghai 201203, China
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Abstract
This review focuses on the steps unique to methionine biosynthesis, namely the conversion of homoserine to methionine. The past decade has provided a wealth of information concerning the details of methionine metabolism and the review focuses on providing a comprehensive overview of the field, emphasizing more recent findings. Details of methionine biosynthesis are addressed along with key cellular aspects, including regulation, uptake, utilization, AdoMet, the methyl cycle, and growing evidence that inhibition of methionine biosynthesis occurs under stressful cellular conditions. The first unique step in methionine biosynthesis is catalyzed by the metA gene product, homoserine transsuccinylase (HTS, or homoserine O-succinyltransferase). Recent experiments suggest that transcription of these genes is indeed regulated by MetJ, although the repressor-binding sites have not yet been verified. Methionine also serves as the precursor of S-adenosylmethionine, which is an essential molecule employed in numerous biological processes. S-adenosylhomocysteine is produced as a consequence of the numerous AdoMet-dependent methyl transfer reactions that occur within the cell. In E. coli and Salmonella, this molecule is recycled in two discrete steps to complete the methyl cycle. Cultures challenged by oxidative stress appear to experience a growth limitation that depends on methionine levels. E. coli that are deficient for the manganese and iron superoxide dismutases (the sodA and sodB gene products, respectively) require the addition of methionine or cysteine for aerobic growth. Modulation of methionine levels in response to stressful conditions further increases the complexity of its regulation.
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11
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Novel broad-spectrum inhibitors of bacterial methionine aminopeptidase. Bioorg Med Chem Lett 2015; 25:3301-6. [PMID: 26099541 DOI: 10.1016/j.bmcl.2015.05.061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 05/20/2015] [Accepted: 05/22/2015] [Indexed: 01/09/2023]
Abstract
With increasing emergence of multi-drug resistant infections, there is a dire need for new classes of compounds that act through unique mechanisms. In this work, we describe the discovery and optimization of a novel series of inhibitors of bacterial methionine aminopeptidase (MAP). Through a high-throughput screening campaign, one azepinone amide hit was found that resembled the native peptide substrate and possessed moderate biochemical potency against three bacterial isozymes. X-ray crystallography was used in combination with substrate-based design to direct the rational optimization of analogs with sub-micromolar potency. The novel compounds presented here represent potent broad-spectrum biochemical inhibitors of bacterial MAP and have the potential to lead to the development of new medicines to combat serious multi-drug resistant infections.
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12
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Arya T, Reddi R, Kishor C, Ganji RJ, Bhukya S, Gumpena R, McGowan S, Drag M, Addlagatta A. Identification of the molecular basis of inhibitor selectivity between the human and streptococcal type I methionine aminopeptidases. J Med Chem 2015; 58:2350-7. [PMID: 25699713 DOI: 10.1021/jm501790e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The methionine aminopeptidase (MetAP) family is responsible for the cleavage of the initiator methionine from newly synthesized proteins. Currently, there are no small molecule inhibitors that show selectivity toward the bacterial MetAPs compared to the human enzyme. In our current study, we have screened 20 α-aminophosphonate derivatives and identified a molecule (compound 15) that selectively inhibits the S. pneumonia MetAP in low micromolar range but not the human enzyme. Further bioinformatics, biochemical, and structural analyses suggested that phenylalanine (F309) in the human enzyme and methionine (M205) in the S. pneumonia MetAP at the analogous position render them with different susceptibilities against the identified inhibitor. X-ray crystal structures of various inhibitors in complex with wild type and F309M enzyme further established the molecular basis for the inhibitor selectivity.
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Affiliation(s)
- Tarun Arya
- Centre for Chemical Biology, CSIR-Indian Institute of Chemical Technology , Hyderabad 500 007, India
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13
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Investigations and design of pyridine-2-carboxylic acid thiazol-2-ylamide analogs as methionine aminopeptidase inhibitors using 3D-QSAR and molecular docking. Med Chem Res 2014. [DOI: 10.1007/s00044-014-0950-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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14
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Sarabia F, Martín-Gálvez F, García-Ruiz C, Sánchez-Ruiz A, Vivar-García C. Epi-, Epoxy-, and C2-Modified Bengamides: Synthesis and Biological Evaluation. J Org Chem 2013; 78:5239-53. [DOI: 10.1021/jo4003272] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Francisco Sarabia
- Department of Organic Chemistry,
Faculty of Sciences, University of Málaga, Campus de Teatinos s/n
29071-Málaga, Spain
| | - Francisca Martín-Gálvez
- Department of Organic Chemistry,
Faculty of Sciences, University of Málaga, Campus de Teatinos s/n
29071-Málaga, Spain
| | - Cristina García-Ruiz
- Department of Organic Chemistry,
Faculty of Sciences, University of Málaga, Campus de Teatinos s/n
29071-Málaga, Spain
| | - Antonio Sánchez-Ruiz
- Department of Organic Chemistry,
Faculty of Sciences, University of Málaga, Campus de Teatinos s/n
29071-Málaga, Spain
| | - Carlos Vivar-García
- Department of Organic Chemistry,
Faculty of Sciences, University of Málaga, Campus de Teatinos s/n
29071-Málaga, Spain
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15
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Martín-Gálvez F, García-Ruiz C, Sánchez-Ruiz A, Valeriote FA, Sarabia F. An array of bengamide E analogues modified at the terminal olefinic position: synthesis and antitumor properties. ChemMedChem 2013; 8:819-31. [PMID: 23512621 DOI: 10.1002/cmdc.201300033] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Indexed: 12/12/2022]
Abstract
Based on our previously described synthetic strategy for bengamide E, a natural product of marine origin with antitumor activity, a small library of analogues modified at the terminal olefinic position was generated with the objective of investigating the effect of structural modifications on antitumor properties. Biological evaluation of these analogues, consisting of IC50 determinations against various tumor cell lines, revealed important aspects with respect to the structural requirements of this olefinic position for activity. Interestingly, the analogue possessing a cyclopentyl group displayed greater potency than the parent bengamide E, representing a key finding upon which to base further investigations into the design of new analogues with promising biological activities.
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Affiliation(s)
- Francisca Martín-Gálvez
- Department of Organic Chemistry, Faculty of Sciences, University of Malaga, Campus de Teatinos s/n. 29071 Málaga, Spain
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16
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Xu W, Lu JP, Ye QZ. Structural analysis of bengamide derivatives as inhibitors of methionine aminopeptidases. J Med Chem 2012; 55:8021-7. [PMID: 22913487 DOI: 10.1021/jm3008695] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Natural-product-derived bengamides possess potent antiproliferative activity and target human methionine aminopeptidases (MetAPs) for their cellular effects. Several derivatives were designed, synthesized, and evaluated as MetAP inhibitors. Here, we present four new X-ray structures of human MetAP1 in complex with the inhibitors. Together with the previous structures of bengamide derivatives with human MetAP2 and tubercular MtMetAP1c, analysis of the interactions of these inhibitors at the active site provides structural basis for further modification of these bengamide inhibitors for improved potency and selectivity as anticancer and antibacterial therapeutics.
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Affiliation(s)
- Wei Xu
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
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17
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Kishor C, Gumpena R, Reddi R, Addlagatta A. Structural studies of Enterococcus faecalis methionine aminopeptidase and design of microbe specific 2,2′-bipyridine based inhibitors. MEDCHEMCOMM 2012. [DOI: 10.1039/c2md20096a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Olaleye O, Raghunand TR, Bhat S, Chong C, Gu P, Zhou J, Zhang Y, Bishai WR, Liu JO. Characterization of clioquinol and analogues as novel inhibitors of methionine aminopeptidases from Mycobacterium tuberculosis. Tuberculosis (Edinb) 2011; 91 Suppl 1:S61-5. [PMID: 22115541 PMCID: PMC11059541 DOI: 10.1016/j.tube.2011.10.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Mycobacterium tuberculosis, the causative agent of tuberculosis claims about five thousand lives daily world-wide, while one-third of the world is infected with dormant tuberculosis. The increased emergence of multi- and extensively drug-resistant strains of M. tuberculosis (Mtb) has heightened the need for novel antimycobacterial agents. Here, we report the discovery of 7-bromo-5-chloroquinolin-8-ol (CLBQ14)-a congener of clioquinol (CQ) as a potent and selective inhibitor of two methionine aminopeptidases (MetAP) from M. tuberculosis: MtMetAP1a and MtMetAP1c. MetAP is a metalloprotease that removes the N-terminal methionine during protein synthesis. N-terminal methionine excision (NME) is a universally conserved process required for the post-translational modification of a significant part of the proteome. The essential role of MetAP in microbes makes it a promising target for the development of new therapeutics. Using a target-based approach in a high-throughput screen, we identified CLBQ14 as a novel MtMetAP inhibitor with higher specificity for both MtMetAP1s relative to their human counterparts. We also found that CLBQ14 is potent against replicating and aged non-growing Mtb at low micro molar concentrations. Furthermore, we observed that the antimycobacterial activity of this pharmacophore correlates well with in vitro enzymatic inhibitory activity. Together, these results revealed a new mode of action of clioquinol and its congeners and validated the therapeutic potential of this pharmacophore for TB chemotherapy.
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Affiliation(s)
- Omonike Olaleye
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX 77004, USA
- Present address: College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX 77004
| | - Tirumalai R. Raghunand
- Center for Tuberculosis Research, Johns Hopkins School of Medicine, Baltimore, MD 21231, USA
- Present address: Center for Cellular and Molecular Biology, Hyderabad, India
| | - Shridhar Bhat
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Curtis Chong
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Present address: Dana Farber Cancer Institute, Harvard Medical School, Boston, MA. Boston, MA 02215-5450, USA
| | - Peihua Gu
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jiangbing Zhou
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Ying Zhang
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - William R. Bishai
- Center for Tuberculosis Research, Johns Hopkins School of Medicine, Baltimore, MD 21231, USA
| | - Jun O. Liu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
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19
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Lu JP, Yuan XH, Ye QZ. Structural analysis of inhibition of Mycobacterium tuberculosis methionine aminopeptidase by bengamide derivatives. Eur J Med Chem 2011; 47:479-84. [PMID: 22118830 DOI: 10.1016/j.ejmech.2011.11.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Revised: 11/03/2011] [Accepted: 11/09/2011] [Indexed: 12/29/2022]
Abstract
Natural product-derived bengamides possess potent antiproliferative activity and target human methionine aminopeptidases for their cellular effects. Using bengamides as a template, several derivatives were designed and synthesized as inhibitors of methionine aminopeptidases of Mycobacterium tuberculosis, and initial antitubercular activity were observed. Here, we present three new X-ray structures of the tubercular enzyme MtMetAP1c in complex with the inhibitors in the Mn(II) form and in the Ni(II) form. All amide moieties of the bengamide derivatives bind to the unique shallow cavity and interact with a flat surface created by His-212 of MtMetAP1c in the Mn(II) form. However, the active site metal has significant influence on the binding mode, because the amide takes a different conformation in the Ni(II) form. The interactions of these inhibitors at the active site provide the structural basis for further modification of these bengamide inhibitors for improved potency and selectivity.
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Affiliation(s)
- Jing-Ping Lu
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, United States
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20
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Wang WL, Chai SC, Ye QZ. Synthesis and biological evaluation of salicylate-based compounds as a novel class of methionine aminopeptidase inhibitors. Bioorg Med Chem Lett 2011; 21:7151-4. [PMID: 22001086 DOI: 10.1016/j.bmcl.2011.09.080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 09/15/2011] [Accepted: 09/19/2011] [Indexed: 12/01/2022]
Abstract
A series of salicylate-based compounds were designed and synthesized based on the simple function group replacement from our previously reported catechol-containing inhibitors of methionine aminopeptidase (MetAP). Some of these salicylate derivatives showed similar potency and metalloform selectivity, and some showed considerable antibacterial activity. These findings are consistent with our previous conclusion that Fe(II) is the likely metal used by MetAP in bacterial cells and provide new lead structures that can be further developed as novel antibacterial agents.
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Affiliation(s)
- Wen-Long Wang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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21
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Growth inhibition of Escherichia coli and methicillin-resistant Staphylococcus aureus by targeting cellular methionine aminopeptidase. Eur J Med Chem 2011; 46:3537-40. [PMID: 21575996 DOI: 10.1016/j.ejmech.2011.04.056] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 04/21/2011] [Accepted: 04/25/2011] [Indexed: 11/23/2022]
Abstract
Methionine aminopeptidase (MetAP) catalyzes the N-terminal methionine excision from the majority of newly synthesized proteins, which is an essential cotranslational process required for cell survival. As such, MetAP has become an appealing target for the development of antimicrobial therapeutics with novel mechanisms of action. By screening a library of small organic molecules, we previously discovered a class of compounds that selectively inhibit the Fe(II)-form of MetAP. Herein, we demonstrate that some of these compounds and their newly synthesized derivatives halt the growth of Escherichia coli and Staphylococcus aureus cells with significant potency. The most potent compound inhibited methicillin-resistant S. aureus (MRSA) growth with an IC(50) value of 1 μM and MIC of 0.7 μg/ml. Two cell-based assays were used to verify that MetAP is the intracellular target in E. coli cells. These findings can serve as foundation for the development of novel therapeutics against an ever increasing threat by drug resistant staphylococcal infections.
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22
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Abstract
Numerous metalloproteins are important therapeutic targets that are gaining increased attention in the medicinal and bioinorganic chemistry communities. This Perspective article describes some emerging trends and recent findings in the area of metalloprotein inhibitor discovery and development. In particular, increasing recognition of the importance of the metal-ligand interactions in these systems calls for more input and consideration from the bioinorganic community to address questions traditionally confined to the medicinal chemistry community.
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Affiliation(s)
| | - Seth M. Cohen
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0358, U.S.A. Fax: 858-822-5598; Tel: 858-822-5596
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23
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Lu JP, Yuan XH, Yuan H, Wang WL, Wan B, Franzblau SG, Ye QZ. Inhibition of Mycobacterium tuberculosis methionine aminopeptidases by bengamide derivatives. ChemMedChem 2011; 6:1041-8. [PMID: 21465667 DOI: 10.1002/cmdc.201100003] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Revised: 03/01/2011] [Indexed: 12/31/2022]
Abstract
Methionine aminopeptidase (MetAP) carries out an essential function of protein N-terminal processing in many bacteria and is a promising target for the development of novel antitubercular agents. Natural bengamides potently inhibit the proliferation of mammalian cells by targeting MetAP enzymes, and the X-ray crystal structure of human type 2 MetAP in complex with a bengamide derivative reveals the key interactions at the active site. By preserving the interactions with the conserved residues inside the binding pocket while exploring the differences between bacterial and human MetAPs around the binding pocket, seven bengamide derivatives were synthesized and evaluated for inhibition of MtMetAP1a and MtMetAP1c in different metalloforms, inhibition of M. tuberculosis growth in replicating and non-replicating states, and inhibition of human K562 cell growth. Potent inhibition of MtMetAP1a and MtMetAP1c and modest growth inhibition of M. tuberculosis were observed for some of these derivatives. Crystal structures of MtMetAP1c in complex with two of the derivatives provided valuable structural information for improvement of these inhibitors for potency and selectivity.
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Affiliation(s)
- Jing-Ping Lu
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA
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24
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Shapiro AB, Gao N, Thresher J, Walkup GK, Whiteaker J. A high-throughput absorbance-based assay for methionine produced by methionine aminopeptidase using S-adenosyl-L-methionine synthetase. ACTA ACUST UNITED AC 2011; 16:494-505. [PMID: 21402755 DOI: 10.1177/1087057111398934] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Methionine aminopeptidase (MAP) (E.C. 3.4.11.18) is a metallopeptidase that cleaves the N-terminal methionine (Met) residue from some proteins. MAP is essential for growth of several bacterial pathogens, making it a target for antibacterial drug discovery. MAP enzymes are also present in eukaryotic cells, and one is a target for antiangiogenic cancer therapy. To screen large compound libraries for MAP inhibitors as the starting point for drug discovery, a high-throughput-compatible assay is valuable. Here the authors describe a novel assay, which detects the Met product of MAP-catalyzed peptide cleavage by coupling it to adenosine triphosphate (ATP)-dependent production of S-adenosyl-L-methionine (SAM) and inorganic phosphate (P(i)) by SAM synthetase (MetK) combined with inorganic pyrophosphatase. The three P(i) ions produced for each Met consumed are detected using Malachite Green/molybdate reagent. This assay can use any unmodified peptide MAP substrate with an N-terminal Met. The assay was used to measure kinetic constants for Escherichia coli MAP using Mn(2+) as the activator and the peptide Met-Gly-Met-Met as the substrate, as well as to measure the potency of a MAP inhibitor. A Mn(2+) buffer is described that can be used to prevent free Mn(2+) depletion by chelating compounds from interfering in screens for MAP inhibitors.
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25
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Jacobsen JA, Fullagar JL, Miller MT, Cohen SM. Identifying chelators for metalloprotein inhibitors using a fragment-based approach. J Med Chem 2010; 54:591-602. [PMID: 21189019 DOI: 10.1021/jm101266s] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Fragment-based lead design (FBLD) has been used to identify new metal-binding groups for metalloenzyme inhibitors. When screened at 1 mM, a chelator fragment library (CFL-1.1) of 96 compounds produced hit rates ranging from 29% to 43% for five matrix metalloproteases (MMPs), 24% for anthrax lethal factor (LF), 49% for 5-lipoxygenase (5-LO), and 60% for tyrosinase (TY). The ligand efficiencies (LE) of the fragment hits are excellent, in the range of 0.4-0.8 kcal/mol. The MMP enzymes all generally elicit the same chelators as hits from CFL-1.1; however, the chelator fragments that inhibit structurally unrelated metalloenzymes (LF, 5-LO, TY) vary considerably. To develop more advanced hits, one hit from CFL-1.1, 8-hydroxyquinoline, was elaborated at four different positions around the ring system to generate new fragments. 8-Hydroxyquinoline fragments substituted at either the 5- or 7-positions gave potent hits against MMP-2, with IC(50) values in the low micromolar range. The 8-hydroxyquinoline represents a promising new chelator scaffold for the development of MMP inhibitors that was discovered by use of a metalloprotein-focused chelator fragment library.
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Affiliation(s)
- Jennifer A Jacobsen
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
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26
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Lu JP, Ye QZ. Expression and characterization of Mycobacterium tuberculosis methionine aminopeptidase type 1a. Bioorg Med Chem Lett 2010; 20:2776-9. [PMID: 20363127 DOI: 10.1016/j.bmcl.2010.03.067] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Revised: 03/17/2010] [Accepted: 03/17/2010] [Indexed: 12/22/2022]
Abstract
Methionine aminopeptidase (MetAP) carries out the cotranslational N-terminal methionine excision and is essential for bacterial survival. Mycobacterium tuberculosis expresses two MetAPs, MtMetAP1a and MtMetAP1c, at different levels in growing and stationary phases, and both are potential targets to develop novel antitubercular therapeutics. Recombinant MtMetAP1a was purified as an apoenzyme, and metal binding and activation were characterized with an activity assay using a fluorogenic substrate. Ni(II), Co(II) and Fe(II) bound tightly at micromolar concentrations, and Ni(II) was the most efficient activator for the MetAP-catalyzed substrate hydrolysis. Although the characteristics of metal binding and activation are similar to MtMetAP1c we characterized before, MtMetAP1a was significantly more active, and more importantly, a set of inhibitors displayed completely different inhibitory profiles on the two mycobacterial MetAPs in both potency and metalloform selectivity. The differences in catalysis and inhibition predicted the significant differences in active site structure.
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Affiliation(s)
- Jing-Ping Lu
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, United States
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27
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Zorzet A, Pavlov MY, Nilsson AI, Ehrenberg M, Andersson DI. Error-prone initiation factor 2 mutations reduce the fitness cost of antibiotic resistance. Mol Microbiol 2010; 75:1299-313. [PMID: 20132454 PMCID: PMC2859245 DOI: 10.1111/j.1365-2958.2010.07057.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/12/2010] [Indexed: 11/27/2022]
Abstract
Mutations in the fmt gene (encoding formyl methionine transferase) that eliminate formylation of initiator tRNA (Met-tRNA(i)) confer resistance to the novel antibiotic class of peptide deformylase inhibitors (PDFIs) while concomitantly reducing bacterial fitness. Here we show in Salmonella typhimurium that novel mutations in initiation factor 2 (IF2) located outside the initiator tRNA binding domain can partly restore fitness of fmt mutants without loss of antibiotic resistance. Analysis of initiation of protein synthesis in vitro showed that with non-formylated Met-tRNA(i) IF2 mutants initiated much faster than wild-type IF2, whereas with formylated fMet-tRNA(i) the initiation rates were similar. Moreover, the increase in initiation rates with Met-tRNA(i) conferred by IF2 mutations in vitro correlated well with the increase in growth rate conferred by the same mutations in vivo, suggesting that the mutations in IF2 compensate formylation deficiency by increasing the rate of in vivo initiation with Met-tRNA(i). IF2 mutants had also a high propensity for erroneous initiation with elongator tRNAs in vitro, which could account for their reduced fitness in vivo in a formylation-proficient strain. More generally, our results suggest that bacterial protein synthesis is mRNA-limited and that compensatory mutations in IF2 could increase the persistence of PDFI-resistant bacteria in clinical settings.
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Affiliation(s)
- Anna Zorzet
- Department of Medical Biochemistry and Microbiology, Uppsala UniversityBox 582, SE-751 23 Uppsala, Sweden
| | - Michael Y Pavlov
- Department of Cell and Molecular Biology, Uppsala UniversityBox 596, SE-751 24 Uppsala, Sweden
| | - Annika I Nilsson
- Department of Medical Biochemistry and Microbiology, Uppsala UniversityBox 582, SE-751 23 Uppsala, Sweden
| | - Måns Ehrenberg
- Department of Cell and Molecular Biology, Uppsala UniversityBox 596, SE-751 24 Uppsala, Sweden
| | - Dan I Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala UniversityBox 582, SE-751 23 Uppsala, Sweden
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28
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Chai SC, Ye QZ. A cell-based assay that targets methionine aminopeptidase in a physiologically relevant environment. Bioorg Med Chem Lett 2010; 20:2129-32. [PMID: 20207144 DOI: 10.1016/j.bmcl.2010.02.052] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Revised: 02/10/2010] [Accepted: 02/10/2010] [Indexed: 11/28/2022]
Abstract
Methionine aminopeptidase (MetAP) is a promising target for the development of novel antibiotics. However, many potent inhibitors of the purified enzyme failed to show significant antibacterial activity. It is uncertain which divalent metal MetAP uses as its native cofactor in bacterial cells. Herein, we describe a cell-based assay that monitors the hydrolysis of a fluorogenic substrate by overexpressed MetAP in permeabilized Escherichia coli cells and its validation with a set of MetAP inhibitors. This cell-based assay is applicable to those cellular targets with poorly defined native cofactor, increasing the chances of identifying inhibitors that can inhibit the cellular target.
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Affiliation(s)
- Sergio C Chai
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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29
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Lu JP, Chai SC, Ye QZ. Catalysis and inhibition of Mycobacterium tuberculosis methionine aminopeptidase. J Med Chem 2010; 53:1329-37. [PMID: 20038112 PMCID: PMC2820511 DOI: 10.1021/jm901624n] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Methionine aminopeptidase (MetAP) carries out an important cotranslational N-terminal methionine excision of nascent proteins and represents a potential target to develop antibacterial and antitubercular drugs. We cloned one of the two MetAPs in Mycobacterium tuberculosis (MtMetAP1c from the mapB gene) and purified it to homogeneity as an apoenzyme. Its activity required a divalent metal ion, and Co(II), Ni(II), Mn(II), and Fe(II) were among activators of the enzyme. Co(II) and Fe(II) had the tightest binding, while Ni(II) was the most efficient cofactor for the catalysis. MtMetAP1c was also functional in E. coli cells because a plasmid-expressed MtMetAP1c complemented the essential function of MetAP in E. coli and supported the cell growth. A set of potent MtMetAP1c inhibitors were identified, and they showed high selectivity toward the Fe(II)-form, the Mn(II)-form, or the Co(II) and Ni(II) forms of the enzyme, respectively. These metalloform selective inhibitors were used to assign the metalloform of the cellular MtMetAP1c. The fact that only the Fe(II)-form selective inhibitors inhibited the cellular MtMetAP1c activity and inhibited the MtMetAP1c-complemented cell growth suggests that Fe(II) is the native metal used by MtMetAP1c in an E. coli cellular environment. Finally, X-ray structures of MtMetAP1c in complex with three metalloform-selective inhibitors were analyzed, which showed different binding modes and different interactions with metal ions and active site residues.
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Affiliation(s)
| | | | - Qi-Zhuang Ye
- To whom correspondence should be addressed: Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202. Tel.: 317-278-0304; Fax: 317-278-4686;
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30
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Olaleye OA, Bishai WR, Liu JO. Targeting the role of N-terminal methionine processing enzymes in Mycobacterium tuberculosis. Tuberculosis (Edinb) 2009; 89 Suppl 1:S55-9. [DOI: 10.1016/s1472-9792(09)70013-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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31
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Skinner-Adams TS, Stack CM, Trenholme KR, Brown CL, Grembecka J, Lowther J, Mucha A, Drag M, Kafarski P, McGowan S, Whisstock JC, Gardiner DL, Dalton JP. Plasmodium falciparum neutral aminopeptidases: new targets for anti-malarials. Trends Biochem Sci 2009; 35:53-61. [PMID: 19796954 DOI: 10.1016/j.tibs.2009.08.004] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2009] [Revised: 08/05/2009] [Accepted: 08/05/2009] [Indexed: 11/19/2022]
Abstract
The neutral aminopeptidases M1 alanyl aminopeptidase (PfM1AAP) and M17 leucine aminopeptidase (PfM17LAP) of the human malaria parasite Plasmodium falciparum are targets for the development of novel anti-malarial drugs. Although the functions of these enzymes remain unknown, they are believed to act in the terminal stages of haemoglobin degradation, generating amino acids essential for parasite growth and development. Inhibitors of both enzymes are lethal to P. falciparum in culture and kill the murine malaria P. chabaudi in vivo. Recent biochemical, structural and functional studies provide the substrate specificity and mechanistic binding data needed to guide the development of more potent anti-malarial drugs. Together with biological studies, these data form the rationale for choosing PfM1AAP and PfM17LAP as targets for anti-malarial development.
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Affiliation(s)
- Tina S Skinner-Adams
- Malaria Biology Laboratory, Queensland Institute of Medical Research, Herston, QLD 4006, Australia.
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32
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Drath M, Baier K, Forchhammer K. An alternative methionine aminopeptidase, MAP-A, is required for nitrogen starvation and high-light acclimation in the cyanobacterium Synechocystis sp. PCC 6803. MICROBIOLOGY-SGM 2009; 155:1427-1439. [PMID: 19359320 DOI: 10.1099/mic.0.026351-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Methionine aminopeptidases (MetAPs or MAPs, encoded by map genes) are ubiquitous and pivotal enzymes for protein maturation in all living organisms. Whereas most bacteria harbour only one map gene, many cyanobacterial genomes contain two map paralogues, the genome of Synechocystis sp. PCC 6803 even three. The physiological function of multiple map paralogues remains elusive so far. This communication reports for the first time differential MetAP function in a cyanobacterium. In Synechocystis sp. PCC 6803, the universally conserved mapC gene (sll0555) is predominantly expressed in exponentially growing cells and appears to be a housekeeping gene. By contrast, expression of mapA (slr0918) and mapB (slr0786) genes increases during stress conditions. The mapB paralogue is only transiently expressed, whereas the widely distributed mapA gene appears to be the major MetAP during stress conditions. A mapA-deficient Synechocystis mutant shows a subtle impairment of photosystem II properties even under non-stressed conditions. In particular, the binding site for the quinone Q(B) is affected, indicating specific N-terminal methionine processing requirements of photosystem II components. MAP-A-specific processing becomes essential under certain stress conditions, since the mapA-deficient mutant is severely impaired in surviving conditions of prolonged nitrogen starvation and high light exposure.
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Affiliation(s)
- Miriam Drath
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Giessen, 35392 Giessen, Germany
| | - Kerstin Baier
- Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Karl Forchhammer
- Institut für Mikrobiologie, Eberhard-Karls-Universität Tübingen, 72076 Tübingen, Germany.,Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Giessen, 35392 Giessen, Germany
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33
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Effects of docosahexaenoic acid on large-conductance Ca2+-activated K+ channels and voltage-dependent K+ channels in rat coronary artery smooth muscle cells. Acta Pharmacol Sin 2009; 30:314-20. [PMID: 19262555 DOI: 10.1038/aps.2009.7] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
AIM To investigate the effects of docosahexaenoic acid (DHA) on large-conductance Ca(2+)-activated K(+)(BK(Ca)) channels and voltage-dependent K(+) (K(V)) channels in rat coronary artery smooth muscle cells (CASMCs). METHODS Rat CASMCs were isolated by an enzyme digestion method. BK(Ca) and K(V) currents in individual CASMCs were recorded by the patch-clamp technique in a whole-cell configuration at room temperature. Effects of DHA on BK(Ca) and K(V) channels were observed when it was applied at 10, 20, 30, 40, 50, 60, 70, and 80 micromol/L. RESULTS When DHA concentrations were greater than 10 micromol/L, BK(Ca) currents increased in a dose-dependent manner. At a testing potential of +80 mV, 6.1%+/-0.3%, 76.5%+/-3.8%, 120.6%+/-5.5%, 248.0%+/-12.3%, 348.7%+/-17.3%, 374.2%+/-18.7%, 432.2%+/-21.6%, and 443.1%+/-22.1% of BK(Ca) currents were increased at the above concentrations, respectively. The half-effective concentration (EC(50)) of DHA on BK(Ca) currents was 37.53+/-1.65 micromol/L. When DHA concentrations were greater than 20 micromol/L, K(V) currents were gradually blocked by increasing concentrations of DHA. At a testing potential of +50 mV, 0.40%+/-0.02%, 1.37%+/-0.06%, 11.80%+/-0.59%, 26.50%+/-1.75%, 56.50%+/-2.89%, 73.30%+/-3.66%, 79.70%+/-3.94%, and 78.1%+/-3.91% of K(V) currents were blocked at the different concentrations listed above, respectively. The EC(50) of DHA on K(V) currents was 44.20+/-0.63 micromol/L. CONCLUSION DHA can activate BK(Ca) channels and block K(V) channels in rat CASMCs, and the EC(50) of DHA for BK(Ca) channels is lower than that for K(V) channels; these findings indicate that the vasorelaxation effects of DHA on vascular smooth muscle cells are mainly due to its activation of BK(Ca) channels.
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Hartley M, Yong W, Bennett B. Heterologous expression and purification of Vibrio proteolyticus (Aeromonas proteolytica) aminopeptidase: a rapid protocol. Protein Expr Purif 2009; 66:91-101. [PMID: 19233285 DOI: 10.1016/j.pep.2009.02.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2009] [Revised: 02/11/2009] [Accepted: 02/11/2009] [Indexed: 11/27/2022]
Abstract
Metalloaminopeptidases (mAPs) are enzymes that are involved in HIV infectivity, tumor growth and metastasis, angiogenesis, and bacterial infection. Investigation of structure-function relationships in mAPs is a prerequisite to rational design of anti-mAP chemotherapeutics. The most intensively studied member of the biomedically important dinuclear mAPs is the prototypical secreted Vibrio proteolyticus di-zinc aminopeptidase (VpAP). The wild-type enzyme is readily purified from the supernatant of cultures of V. proteolyticus, but recombinant variants require expression in Escherichia coli. A greatly improved system for the purification of recombinant VpAP is described. A VpAP-(His)(6) polypeptide, containing an N-terminal propeptide, and a C-terminal (His)(6) adduct, was purified by metal ion affinity chromatography from the supernatant of cultures of E. coli. This single step replaced the sequence of (NH(4))(2)SO(4) fractionation, and anion-exchange and hydrophobic interaction chromatographic separations of earlier methods. Traditionally, recombinant VpAP proenzyme has been treated with proteinase K and with heat (70 degrees C), to remove the N- and C-terminal regions, and yield the mature active enzyme. This method is unsuitable for VpAP variants that are unstable towards these treatments. In the new method, the hitherto noted, but not fully appreciated, ability of VpAP to autocatalyze the hydrolysis of the N-terminal propeptide and C-terminal regions was exploited; extensive dialysis of the highly purified VpAP-(His)(6) full-length polypeptide yielded the mature active protein without recourse to proteinase K or heat treatment. Purification of variants that have previously defied isolation as mature forms of the protein was thus carried out.
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Affiliation(s)
- Mariam Hartley
- Department of Biophysics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226-0509, USA
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35
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Wang WL, Chai SC, Ye QZ. Synthesis and structure-function analysis of Fe(II)-form-selective antibacterial inhibitors of Escherichia coli methionine aminopeptidase. Bioorg Med Chem Lett 2009; 19:1080-3. [PMID: 19167218 DOI: 10.1016/j.bmcl.2009.01.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2008] [Revised: 01/05/2009] [Accepted: 01/06/2009] [Indexed: 11/18/2022]
Abstract
Methionine aminopeptidase (MetAP) is a promising target for the development of novel antibacterial, antifungal and anticancer therapy. Based on our previous results, catechol derivatives coupled with a thiazole or thiophene moiety showed high potency and selectivity toward the Fe(II)-form of Escherichia coli MetAP, and some of them clearly showed antibacterial activity, indicating that Fe(II) is likely the physiologically relevant metal for MetAP in E. coli and other bacterial cells. To further understand the structure-function relationship of these Fe(II)-form selective MetAP inhibitors, a series of catechol derivatives was designed and synthesized by replacement of the thiazole or thiophene moiety with different five-membered and six-membered heterocycles. Inhibitory activities of these newly synthesized MetAP inhibitors indicate that many five- and six-membered rings can be accommodated by MetAP and potency on the Fe(II)-form can be improved by introducing substitutions on the heterocyles to explore additional interactions with the enzyme. The furan-containing catechols 11-13 showed the highest potency at 1muM on the Fe(II)-form MetAP, and they were also among the best inhibitors for growth inhibition against E. coli AS19 strain. These findings provide useful information for the design and discovery of more effective MetAP inhibitors for therapeutic applications.
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Affiliation(s)
- Wen-Long Wang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA
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36
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Green LS, Bullard JM, Ribble W, Dean F, Ayers DF, Ochsner UA, Janjic N, Jarvis TC. Inhibition of methionyl-tRNA synthetase by REP8839 and effects of resistance mutations on enzyme activity. Antimicrob Agents Chemother 2009; 53:86-94. [PMID: 19015366 PMCID: PMC2612134 DOI: 10.1128/aac.00275-08] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2008] [Revised: 06/09/2008] [Accepted: 10/22/2008] [Indexed: 11/20/2022] Open
Abstract
REP8839 is a selective inhibitor of methionyl-tRNA synthetase (MetRS) with antibacterial activity against a variety of gram-positive organisms. We determined REP8839 potency against Staphylococcus aureus MetRS and assessed its selectivity for bacterial versus human orthologs of MetRS. The inhibition constant (K(i)) of REP8839 was 10 pM for Staphylococcus aureus MetRS. Inhibition of MetRS by REP8839 was competitive with methionine and uncompetitive with ATP. Thus, high physiological ATP levels would actually facilitate optimal binding of the inhibitor. While many gram-positive bacteria, such as Staphylococcus aureus, express exclusively the MetRS1 subtype, many gram-negative bacteria express an alternative homolog called MetRS2. Some gram-positive bacteria, such as Streptococcus pneumoniae and Bacillus anthracis, express both MetRS1 and MetRS2. MetRS2 orthologs were considerably less susceptible to REP8839 inhibition. REP8839 inhibition of human mitochondrial MetRS was 1,000-fold weaker than inhibition of Staphylococcus aureus MetRS; inhibition of human cytoplasmic MetRS was not detectable, corresponding to >1,000,000-fold selectivity for the bacterial target relative to its cytoplasmic counterpart. Mutations in MetRS that confer reduced susceptibility to REP8839 were examined. The mutant MetRS enzymes generally exhibited substantially impaired catalytic activity, particularly in aminoacylation turnover rates. REP8839 K(i) values ranged from 4- to 190,000-fold higher for the mutant enzymes than for wild-type MetRS. These observations provide a potential mechanistic explanation for the reduced growth fitness observed with MetRS mutant strains relative to that with wild-type Staphylococcus aureus.
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37
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Wang WL, Chai SC, Huang M, He HZ, Hurley TD, Ye QZ. Discovery of inhibitors of Escherichia coli methionine aminopeptidase with the Fe(II)-form selectivity and antibacterial activity. J Med Chem 2008; 51:6110-20. [PMID: 18785729 DOI: 10.1021/jm8005788] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Methionine aminopeptidase (MetAP) is a promising target to develop novel antibiotics, because all bacteria express MetAP from a single gene that carries out the essential function of removing N-terminal methionine from nascent proteins. Divalent metal ions play a critical role in the catalysis, and there is an urgent need to define the actual metal used by MetAP in bacterial cells. By high throughput screening, we identified a novel class of catechol-containing MetAP inhibitors that display selectivity for the Fe(II)-form of MetAP. X-ray structure revealed that the inhibitor binds to MetAP at the active site with the catechol coordinating to the metal ions. Importantly, some of the inhibitors showed antibacterial activity at low micromolar concentration on Gram-positive and Gram-negative bacteria. Our data indicate that Fe(II) is the likely metal used by MetAP in the cellular environment, and MetAP inhibitors need to inhibit this metalloform of MetAP effectively to be therapeutically useful.
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Affiliation(s)
- Wen-Long Wang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
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38
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Chai SC, Wang WL, Ye QZ. FE(II) is the native cofactor for Escherichia coli methionine aminopeptidase. J Biol Chem 2008; 283:26879-85. [PMID: 18669631 DOI: 10.1074/jbc.m804345200] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Divalent metal ions play a critical role in the removal of N-terminal methionine from nascent proteins by methionine aminopeptidase (MetAP). Being an essential enzyme for bacteria, MetAP is an appealing target for the development of novel antibacterial drugs. Although purified enzyme can be activated by several divalent metal ions, the exact metal ion used by MetAP in cells is unknown. Many MetAP inhibitors are highly potent on purified enzyme, but they fail to show significant inhibition of bacterial growth. One possibility for the failure is a disparity of the metal used in activation of purified MetAP and the metal actually used by MetAP inside bacterial cells. Therefore, the challenge is to elucidate the physiologically relevant metal for MetAP and discover MetAP inhibitors that can effectively inhibit cellular MetAP. We have recently discovered MetAP inhibitors with selectivity toward different metalloforms of Escherichia coli MetAP, and with these unique inhibitors, we characterized their inhibition of MetAP enzyme activity in a cellular environment. We observed that only inhibitors that are selective for the Fe(II)-form of MetAP were potent in this assay. Further, we found that only these Fe(II)-form selective inhibitors showed significant inhibition of growth of five E. coli strains and two Bacillus strains. We confirmed their cellular target as MetAP by analysis of N-terminal processed and unprocessed recombinant glutathione S-transferase proteins. Therefore, we conclude that Fe(II) is the likely metal used by MetAP in E. coli and other bacterial cells.
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Affiliation(s)
- Sergio C Chai
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
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Narayanan SS, Ramanujan A, Krishna S, Nampoothiri KM. Purification and biochemical characterization of methionine aminopeptidase (MetAP) from Mycobacterium smegmatis mc2155. Appl Biochem Biotechnol 2008; 151:512-21. [PMID: 18594775 DOI: 10.1007/s12010-008-8227-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2007] [Accepted: 03/20/2008] [Indexed: 11/26/2022]
Abstract
The methionine aminopeptidase (MetAP) catalyzes the removal of amino terminal methionine from newly synthesized polypeptide. MetAP from Mycobacterium smegmatis mc(2) 155 was purified from the culture lysate in four sequential steps to obtain a final purification fold of 22. The purified enzyme exhibited a molecular weight of approximately 37 kDa on sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Activity staining was performed to detect the methionine aminopeptidase activity on native polyacrylamide gel. The enzyme was characterized biochemically, using L-methionine p-nitroanilide as substrate. The enzyme was found to have a temperature and pH optimum of 50 degrees C and 8.5, respectively, and was found to be stable at 50 degrees C with half-life more than 8 h. The enzyme activity was enhanced by Mg(2+) and Co(2+) and was inhibited by Fe(2+) and Cu(2+). The enzyme activity inhibited by EDTA is restored in presence of Mg(2+) suggesting the possible role of Mg(2+) as metal cofactor of the enzyme in vitro.
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Affiliation(s)
- Sai Shyam Narayanan
- Biotechnology Division, National Institute for Interdisciplinary Science and Technology, Trivandrum, Kerala, India
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40
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Brandi L, Fabbretti A, Pon CL, Dahlberg AE, Gualerzi CO. Initiation of protein synthesis: a target for antimicrobials. Expert Opin Ther Targets 2008; 12:519-34. [PMID: 18410237 DOI: 10.1517/14728222.12.5.519] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
BACKGROUND Translation initiation is a basic and universal biological process that employs significantly different components and displays substantially different mechanisms in bacterial, archaeal and eukaryotic cells. A large amount of detailed mechanistic and structural information on the bacterial translation initiation apparatus has been uncovered in recent years. OBJECTIVE to understand which translation initiation steps could represent a novel or underexploited target for the discovery of new and specific antibacterial drugs. METHODS Brief descriptions of the properties and mechanism of action of the major antibiotics that have a documented direct inhibitory effect on bacterial translation initiation are presented. RESULTS/CONCLUSIONS Considerations and predictions concerning a future scenario for research and identification of bacterial translation initiation inhibitors are presented.
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Vedantham P, Guerra JM, Schoenen F, Huang M, Gor PJ, Georg GI, Wang JL, Neuenswander B, Lushington GH, Mitscher LA, Ye QZ, Hanson PR. Ionic immobilization, diversification, and release: application to the generation of a library of methionine aminopeptidase inhibitors. ACTA ACUST UNITED AC 2007; 10:185-94. [PMID: 18163595 DOI: 10.1021/cc700085c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Development of an ionic immobilization, diversification, and release method for the generation of methionine aminopeptidase inhibitors is reported. This method involves the immobilization of 5-bromofuran-2-carboxylic acid and 5-bromothiophene-2-carboxylic acid onto PS-BEMP, followed by Suzuki reaction on a resin-bound intermediate and subsequent release to provide products in moderate yields and excellent purities. Compound potencies were evaluated on the Co(II), Mn(II), Ni(II), and Fe(II) forms of Escherichia coli MetAP1. The furoic-acid analogs were found to be Mn(II) selective with IC 50 values in the low micromolar range. Qualitative SAR analysis, supplemented by molecular modeling studies, provides valuable information on structural elements responsible for potency and selectivity.
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Affiliation(s)
- Punitha Vedantham
- Department of Chemistry, University of Kansas, 1251 Wescoe Hall Drive, Lawrence, Kansas 66045, USA
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Ma ZQ, Xie SX, Huang QQ, Nan FJ, Hurley TD, Ye QZ. Structural analysis of inhibition of E. coli methionine aminopeptidase: implication of loop adaptability in selective inhibition of bacterial enzymes. BMC STRUCTURAL BIOLOGY 2007; 7:84. [PMID: 18093325 PMCID: PMC2238726 DOI: 10.1186/1472-6807-7-84] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2007] [Accepted: 12/19/2007] [Indexed: 11/17/2022]
Abstract
Background Methionine aminopeptidase is a potential target of future antibacterial and anticancer drugs. Structural analysis of complexes of the enzyme with its inhibitors provides valuable information for structure-based drug design efforts. Results Five new X-ray structures of such enzyme-inhibitor complexes were obtained. Analysis of these and other three similar structures reveals the adaptability of a surface-exposed loop bearing Y62, H63, G64 and Y65 (the YHGY loop) that is an integral part of the substrate and inhibitor binding pocket. This adaptability is important for accommodating inhibitors with variations in size. When compared with the human isozymes, this loop either becomes buried in the human type I enzyme due to an N-terminal extension that covers its position or is replaced by a unique insert in the human type II enzyme. Conclusion The adaptability of the YHGY loop in E. coli methionine aminopeptidase, and likely in other bacterial methionine aminopeptidases, enables the enzyme active pocket to accommodate inhibitors of differing size. The differences in this adaptable loop between the bacterial and human methionine aminopeptidases is a structural feature that can be exploited to design inhibitors of bacterial methionine aminopeptidases as therapeutic agents with minimal inhibition of the corresponding human enzymes.
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Affiliation(s)
- Ze-Qiang Ma
- High Throughput Screening Laboratory, University of Kansas, Lawrence, Kansas 66047, USA.
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43
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Hu X, Dang Y, Tenney K, Crews P, Tsai CW, Sixt KM, Cole PA, Liu JO. Regulation of c-Src nonreceptor tyrosine kinase activity by bengamide A through inhibition of methionine aminopeptidases. ACTA ACUST UNITED AC 2007; 14:764-74. [PMID: 17656313 PMCID: PMC3165037 DOI: 10.1016/j.chembiol.2007.05.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2007] [Revised: 05/07/2007] [Accepted: 05/24/2007] [Indexed: 11/17/2022]
Abstract
Methionine aminopeptidases (MetAPs) remove the N-terminal initiator methionine during protein synthesis, a prerequisite step for N-terminal myristoylation. N-myristoylation of proto-oncogene c-Src is essential for its membrane association and proper signal transduction. We used bengamides, a family of general MetAP inhibitors, to understand the downstream physiological functions of MetAPs. c-Src from bengamide A-treated cells retained its N-terminal methionine and suffered a decrease in N-terminal myristoylation, which was accompanied by a shift of its subcellular distribution from the plasma membrane to the cytosol. Furthermore, bengamide A decreased the tyrosine kinase activities of c-Src both in vitro and in vivo and eventually delayed cell-cycle progression through G(2)/M. Thus, c-Src is a physiologically relevant substrate for MetAPs whose dysfunction is likely to account for the cell-cycle effects of MetAP inhibitors including bengamide A.
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Affiliation(s)
- Xiaoyi Hu
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University, School of Medicine, 725 N. Wolfe St. Baltimore, MD 21205
| | - Yongjun Dang
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University, School of Medicine, 725 N. Wolfe St. Baltimore, MD 21205
| | - Karen Tenney
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064
| | - Phillip Crews
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064
| | - Chiawei W. Tsai
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University, School of Medicine, 725 N. Wolfe St. Baltimore, MD 21205
| | - Katherine M. Sixt
- Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University, School of Medicine, 725 N. Wolfe St. Baltimore, MD 21205
| | - Philip A. Cole
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University, School of Medicine, 725 N. Wolfe St. Baltimore, MD 21205
| | - Jun O. Liu
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University, School of Medicine, 725 N. Wolfe St. Baltimore, MD 21205
- Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University, School of Medicine, 725 N. Wolfe St. Baltimore, MD 21205
- Correspondence: Dr. Jun O. Liu, , (410)-955-4619
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Mills JS. Differential activation of polymorphisms of the formyl peptide receptor by formyl peptides. Biochim Biophys Acta Mol Basis Dis 2007; 1772:1085-92. [PMID: 17644322 PMCID: PMC2094211 DOI: 10.1016/j.bbadis.2007.06.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2007] [Revised: 06/01/2007] [Accepted: 06/04/2007] [Indexed: 11/26/2022]
Abstract
We have investigated the role of two polymorphic sites (R190W and N192K) on the binding and activation of the formyl peptide receptor (FPR) by viral and formyl peptides. WEDWVGWI, a peptide with antiviral activity derived from the membrane proximal region of feline immunodeficiency virus, binds with high affinity to FPR. The three tryptophans in the peptide are all essential for FPR binding, just as they were essential for antiviral activity [S. Giannecchini, A. Di Fenza, A.M. D'Ursi, D. Matteucci, P. Rovero, M. Bendinelli, Antiviral activity and conformational features of an octapeptide derived from the membrane-proximal ectodomain of the feline immunodeficiency virus transmembrane glycoprotein, J. Virol. 77 (2003) 3724]. Formyl-NleWEDWVGWI behaved as a weak partial agonist with FPR W190/N192 but a stronger partial agonist with FPR R190/K192 and FPR R190/N192. Formyl-NleNleWEDWVGWI behaved as a full agonist toward all three FPRs but exhibited a much higher EC(50) with W190/N192 FPR (300+/-45 nM) than for R190/K192 FPR (40+/-3 nM) or R190/N192 (60+/-8 nM). Formyl-MYKWPWYVWL preferentially activated R190/K192 and R190/N192 FPRs by>5 fold compared to W190/N192 FPR. Formyl-MFEDAVAWF, a peptide derived from a protein in Mycobacterium avium subsp. paratuberculosis and formyl-MFTFEPFPTN, a peptide derived from the N-terminus of chemotaxis inhibitory protein of Staphylococcus aureus with an added N-terminal formyl-methionine exhibited the greatest selectivity for R190/K192 and R190/N192 FPRs with approximately 10 fold lower EC(50)s than that observed with FPR W190/N192. Thus, individuals with the W190 polymorphism may display a reduced ability to detect certain formyl peptides.
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Key Words
- fpr, formyl peptide receptor
- chips, chemotaxis inhibitory protein of staphylococcus aureus
- cho s, chinese hamster ovary cells designed for suspension culture
- hrsv, human respiratory syncytial virus
- fiv, feline immunodeficiency virus
- fmlf, n-formyl-methionyl-leucyl-phenylalanine
- flipr, fprl1 inhibitory protein
- aids, acquired immunodeficiency syndrome
- siv, simian immunodeficiency virus
- hiv, human immunodeficiency virus
- sars, severe acute respiratory syndrome
- gp-41, 41 kilodalton glycoprotein
- gp-36, 36 kilodalton glycoprotein
- hr, heptade repeat
- fitc, fluorescein isothiocyanate
- formyl-nle-leu-phe-nle-tyr-lys-fitc, formyl-nle-leu-phe-nle-tyr-lys labeled at the lys residue with fluorescein isothiocyanate
- formyl-nle-leu-phe-nle-tyr-lys, labeled at the lys residue with alexa fluor n-hydroxy-succinimide
- fmlf, formyl-met-leu-phe
- tmh, transmembrane helix
- fprl1, formyl peptide receptor like 1
- gtpγs, guanosine 5′-3-o-(thio)triphosphate
- formyl peptides
- signal transduction
- g protein-coupled receptor
- polymorphism
- feline immunodeficiency virus
- chemotaxis inhibitory protein of staphylococcus aureus
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Affiliation(s)
- John S Mills
- Montana State University, 109 Lewis Hall, Bozeman, MT 59717-3520, USA.
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Evdokimov AG, Pokross M, Walter RL, Mekel M, Barnett BL, Amburgey J, Seibel WL, Soper SJ, Djung JF, Fairweather N, Diven C, Rastogi V, Grinius L, Klanke C, Siehnel R, Twinem T, Andrews R, Curnow A. Serendipitous discovery of novel bacterial methionine aminopeptidase inhibitors. Proteins 2007; 66:538-46. [PMID: 17120228 DOI: 10.1002/prot.21207] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In this article we describe the application of structural biology methods to the discovery of novel potent inhibitors of methionine aminopeptidases. These enzymes are employed by the cells to cleave the N-terminal methionine from nascent peptides and proteins. As this is one of the critical steps in protein maturation, it is very likely that inhibitors of these enzymes may prove useful as novel antibacterial agents. Involvement of crystallography at the very early stages of the inhibitor design process resulted in serendipitous discovery of a new inhibitor class, the pyrazole-diamines. Atomic-resolution structures of several inhibitors bound to the enzyme illuminate a new mode of inhibitor binding.
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Affiliation(s)
- Artem G Evdokimov
- Structural Biology Core Facility, The Procter & Gamble Pharmaceuticals, Mason, Ohio 45040, USA.
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46
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Warren GL, Andrews CW, Capelli AM, Clarke B, LaLonde J, Lambert MH, Lindvall M, Nevins N, Semus SF, Senger S, Tedesco G, Wall ID, Woolven JM, Peishoff CE, Head MS. A critical assessment of docking programs and scoring functions. J Med Chem 2006; 49:5912-31. [PMID: 17004707 DOI: 10.1021/jm050362n] [Citation(s) in RCA: 1165] [Impact Index Per Article: 64.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Docking is a computational technique that samples conformations of small molecules in protein binding sites; scoring functions are used to assess which of these conformations best complements the protein binding site. An evaluation of 10 docking programs and 37 scoring functions was conducted against eight proteins of seven protein types for three tasks: binding mode prediction, virtual screening for lead identification, and rank-ordering by affinity for lead optimization. All of the docking programs were able to generate ligand conformations similar to crystallographically determined protein/ligand complex structures for at least one of the targets. However, scoring functions were less successful at distinguishing the crystallographic conformation from the set of docked poses. Docking programs identified active compounds from a pharmaceutically relevant pool of decoy compounds; however, no single program performed well for all of the targets. For prediction of compound affinity, none of the docking programs or scoring functions made a useful prediction of ligand binding affinity.
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Affiliation(s)
- Gregory L Warren
- GlaxoSmithKline Pharmaceuticals, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, USA.
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Abstract
Researchers in the post-genome era are confronted with the daunting task of assigning structure and function to tens of thousands of encoded proteins. To realize this goal, new technologies are emerging for the analysis of protein function on a global scale, such as activity-based protein profiling (ABPP), which aims to develop active site-directed chemical probes for enzyme analysis in whole proteomes. For the pursuit of such chemical proteomic technologies, it is helpful to derive inspiration from protein-reactive natural products. Natural products use a remarkably diverse set of mechanisms to covalently modify enzymes from distinct mechanistic classes, thus providing a wellspring of chemical concepts that can be exploited for the design of active-site-directed proteomic probes. Herein, we highlight several examples of protein-reactive natural products and illustrate how their mechanisms of action have influenced and continue to shape the progression of chemical proteomic technologies like ABPP.
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Affiliation(s)
- Carmen Drahl
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
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Chen X, Chong CR, Shi L, Yoshimoto T, Sullivan DJ, Liu JO. Inhibitors of Plasmodium falciparum methionine aminopeptidase 1b possess antimalarial activity. Proc Natl Acad Sci U S A 2006; 103:14548-53. [PMID: 16983082 PMCID: PMC1599997 DOI: 10.1073/pnas.0604101103] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
With >1 million deaths annually, mostly among children in sub-Saharan Africa, malaria poses one of the most critical challenges in medicine today. Although introduction of the artemisinin class of antimalarial drugs has offered a temporary solution to the problem of drug resistance, new antimalarial drugs are needed to ensure effective control of the disease in the future. Herein, we have investigated members of the methionine aminopeptidase family as potential antimalarial targets. The Plasmodium falciparum methionine aminopeptidase 1b (PfMetAP1b), one of four MetAP proteins encoded in the P. falciparum genome, was cloned, overexpressed, purified, and used to screen a 175,000-compound library for inhibitors. A family of structurally related inhibitors containing a 2-(2-pyridinyl)-pyrimidine core was identified. Structure/activity studies led to the identification of a potent PfMetAP1b inhibitor, XC11, with an IC(50) of 112 nM. XC11 was highly selective for PfMetAP1b and did not exhibit significant cytotoxicity against primary human fibroblasts. Most importantly, XC11 inhibited the proliferation of P. falciparum strains 3D7 [chloroquine (CQ)-sensitive] and Dd2 (multidrug-resistant) in vitro and is active in mouse malaria models for both CQ-sensitive and CQ-resistant strains. These results suggest that PfMetAP1b is a promising target and XC11 is an important lead compound for the development of novel antimalarial drugs.
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Affiliation(s)
- Xiaochun Chen
- Departments of *Pharmacology and Molecular Sciences and
| | | | - Lirong Shi
- The Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205; and
| | - Tadashi Yoshimoto
- School of Pharmaceutical Sciences, Nagasaki University, Nagasaki 852-8521, Japan
| | - David J. Sullivan
- The Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205; and
| | - Jun O. Liu
- Departments of *Pharmacology and Molecular Sciences and
- Oncology and
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205
- To whom correspondence should be addressed. E-mail:
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Ye QZ, Xie SX, Ma ZQ, Huang M, Hanzlik RP. Structural basis of catalysis by monometalated methionine aminopeptidase. Proc Natl Acad Sci U S A 2006; 103:9470-5. [PMID: 16769889 PMCID: PMC1480431 DOI: 10.1073/pnas.0602433103] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Methionine aminopeptidase (MetAP) removes the amino-terminal methionine residue from newly synthesized proteins, and it is a target for the development of antibacterial and anticancer agents. Available x-ray structures of MetAP, as well as other metalloaminopeptidases, show an active site containing two adjacent divalent metal ions bridged by a water molecule or hydroxide ion. The predominance of dimetalated structures leads naturally to proposed mechanisms of catalysis involving both metal ions. However, kinetic studies indicate that in many cases, only a single metal ion is required for full activity. By limiting the amount of metal ion present during crystal growth, we have now obtained a crystal structure for a complex of Escherichia coli MetAP with norleucine phosphonate, a transition-state analog, and only a single Mn(II) ion bound at the active site in the position designated M1, and three related structures of the same complex that show the transition from the mono-Mn(II) form to the di-Mn(II) form. An unliganded structure was also solved. In view of the full kinetic competence of the monometalated MetAP, the much weaker binding constant for occupancy of the M2 site compared with the M1 site, and the newly determined structures, we propose a revised mechanism of peptide bond hydrolysis by E. coli MetAP. We also suggest that the crystallization of dimetalated forms of metallohydrolases may, in some cases, be a misleading experimental artifact, and caution must be taken when structures are generated to aid in elucidation of reaction mechanisms or to support structure-aided drug design efforts.
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Affiliation(s)
- Qi-Zhuang Ye
- High Throughput Screening Laboratory and Department of Medicinal Chemistry, University of Kansas, 1501 Wakarusa Drive, Lawrence, KS 66045, USA.
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Nampoothiri KM, Nagy V, Kovacs K, Szakacs G, Pandey A. l-leucine aminopeptidase production by filamentous Aspergillus fungi. Lett Appl Microbiol 2005; 41:498-504. [PMID: 16305677 DOI: 10.1111/j.1472-765x.2005.01789.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
AIMS To screen various filamentous fungi belonging to Aspergillus spp. producing leucine and methionine aminopeptidases. METHODS AND RESULTS Twenty-eight Aspergillus strains representing 14 species within the genus were screened for L-leucine aminopeptidase (LAP) production in two media in shake flask fermentation. Two Aspergillus sojae (NRRL 1988 and NRRL 6271) and one Aspergillus oryzae (NRRL 6270) strains were selected as the best producers for further studies. The peak LAP activities were 2.61, 2.59 and 1.30 IU ml(-1) for the three fungi on days 2, 5 and 4 respectively. In addition to LAP, L-methionine aminopeptidase (MAP) activity was also detected. Apart from submerged fermentation, the highest LAP yields by solid-state fermentation were 11.39, 17.40 and 13.02 IU g(-1) dry matter for the above fungi. The temperature and pH optimum of the enzyme was found to be in the range of 65-75 degrees C at pH 8.0-9.0 for all three fungi. Metal ions, Co(2+) and Fe(2+) in 2 mmol l(-1) concentration apparently enhanced the relative enzyme activity and heat stability. CONCLUSIONS Two A. sojae (NRRL 1988 and NRRL 6271) and one A. oryzae (NRRL 6270) strains were found to be the best producers of LAP and MAP. The preliminary characterization studies revealed that the enzyme is considerably thermostable and belongs to the class metalloenzymes. SIGNIFICANCE AND IMPACT OF THE STUDY A good number of aspergilli were screened and the ability of the fungal aminopeptidase to release a particular N-terminal amino acid along with its high thermal stability, makes them interesting for controlling the degree of hydrolysis and flavour development for a wide range of substrate.
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Affiliation(s)
- K M Nampoothiri
- Biotechnology Division, Regional Research Laboratory (CSIR), Trivandrum, Kerala, India.
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