1
|
Harshaw NS, Meyer MD, Stella NA, Lehner KM, Kowalski RP, Shanks RMQ. The Short-chain Fatty Acid Propionic Acid Activates the Rcs Stress Response System Partially through Inhibition of d-Alanine Racemase. mSphere 2023; 8:e0043922. [PMID: 36645277 PMCID: PMC9942566 DOI: 10.1128/msphere.00439-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 12/16/2022] [Indexed: 01/17/2023] Open
Abstract
The Enterobacterial Rcs stress response system reacts to envelope stresses through a complex two-component phosphorelay system to regulate a variety of environmental response genes, such as capsular polysaccharide and flagella biosynthesis genes. However, beyond Escherichia coli, the stresses that activate Rcs are not well-understood. In this study, we used a Rcs system-dependent luminescent transcriptional reporter to screen a library of over 240 antimicrobial compounds for those that activated the Rcs system in Serratia marcescens, a Yersiniaceae family bacterium. Using an isogenic rcsB mutant to establish specificity, both new and expected activators were identified, including the short-chain fatty acid propionic acid, which is found at millimolar levels in the human gut. Propionic acid did not reduce the bacterial intracellular pH, as was hypothesized for its antibacterial mechanism. Instead, data suggest that the Rcs-activation by propionic acid is due, in part, to an inactivation of alanine racemase. This enzyme is responsible for the biosynthesis of d-alanine, which is an amino-acid that is required for the generation of bacterial cell walls. Consistent with what was observed in S. marcescens, in E. coli, alanine racemase mutants demonstrated elevated expression of the Rcs-reporter in a d-alanine-dependent and RcsB-dependent manner. These results suggest that host gut short-chain fatty acids can influence bacterial behavior via the activation of the Rcs stress response system. IMPORTANCE The Rcs bacterial stress response system responds to envelope stresses by globally altering gene expression to profoundly impact host-pathogen interactions, virulence, and antibiotic tolerance. In this study, a luminescent Rcs-reporter plasmid was used to screen a library of compounds for activators of Rcs. Among the strongest inducers was the short-chain fatty acid propionic acid, which is found at high concentrations in the human gut. This study suggests that gut short-chain fatty acids can affect both bacterial virulence and antibiotic tolerance via the induction of the Rcs system.
Collapse
Affiliation(s)
- Nathaniel S. Harshaw
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Mitchell D. Meyer
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Nicholas A. Stella
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Kara M. Lehner
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Regis P. Kowalski
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Robert M. Q. Shanks
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| |
Collapse
|
2
|
Pfanzelt M, Maher TE, Absmeier RM, Schwarz M, Sieber SA. Tailored Pyridoxal Probes Unravel Novel Cofactor-Dependent Targets and Antibiotic Hits in Critical Bacterial Pathogens. Angew Chem Int Ed Engl 2022; 61:e202117724. [PMID: 35199904 PMCID: PMC9321722 DOI: 10.1002/anie.202117724] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Indexed: 01/21/2023]
Abstract
Unprecedented bacterial targets are urgently needed to overcome the resistance crisis. Herein we systematically mine pyridoxal phosphate‐dependent enzymes (PLP‐DEs) in bacteria to focus on a target class which is involved in crucial metabolic processes. For this, we tailored eight pyridoxal (PL) probes bearing modifications at various positions. Overall, the probes exceeded the performance of a previous generation and provided a detailed map of PLP‐DEs in clinically relevant pathogens including challenging Gram‐negative strains. Putative PLP‐DEs with unknown function were exemplarily characterized via in‐depth enzymatic assays. Finally, we screened a panel of PLP binders for antibiotic activity and unravelled the targets of hit molecules. Here, an uncharacterized enzyme, essential for bacterial growth, was assigned as PLP‐dependent cysteine desulfurase and confirmed to be inhibited by the marketed drug phenelzine. Our approach provides a basis for deciphering novel PLP‐DEs as essential antibiotic targets along with corresponding ways to decipher small molecule inhibitors.
Collapse
Affiliation(s)
- Martin Pfanzelt
- Center for Functional Protein Assemblies (CPA), Department of Chemistry, Chair of Organic Chemistry II, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748, Garching, Germany
| | - Thomas E Maher
- Center for Functional Protein Assemblies (CPA), Department of Chemistry, Chair of Organic Chemistry II, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748, Garching, Germany.,Department of Chemistry, Molecular Sciences Research Hub, White City Campus and Institute of Chemical Biology, Molecular Sciences Research Hub, White City Campus, Imperial College London, 82 Wood Lane, London, W12 0BZ, UK
| | - Ramona M Absmeier
- Center for Functional Protein Assemblies (CPA), Department of Chemistry, Chair of Organic Chemistry II, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748, Garching, Germany
| | - Markus Schwarz
- Center for Functional Protein Assemblies (CPA), Department of Chemistry, Chair of Organic Chemistry II, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748, Garching, Germany
| | - Stephan A Sieber
- Center for Functional Protein Assemblies (CPA), Department of Chemistry, Chair of Organic Chemistry II, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748, Garching, Germany
| |
Collapse
|
3
|
Nakamura R, Ogawa S, Takahashi Y, Fujishiro T. Cycloserine enantiomers inhibit PLP‐dependent cysteine desulfurase SufS via distinct mechanisms. FEBS J 2022; 289:5947-5970. [DOI: 10.1111/febs.16455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 03/20/2022] [Accepted: 04/07/2022] [Indexed: 01/31/2023]
Affiliation(s)
- Ryosuke Nakamura
- Department of Biochemistry and Molecular Biology Graduate School of Science and Engineering Saitama University Japan
| | - Shoko Ogawa
- Department of Biochemistry and Molecular Biology Graduate School of Science and Engineering Saitama University Japan
| | - Yasuhiro Takahashi
- Department of Biochemistry and Molecular Biology Graduate School of Science and Engineering Saitama University Japan
| | - Takashi Fujishiro
- Department of Biochemistry and Molecular Biology Graduate School of Science and Engineering Saitama University Japan
| |
Collapse
|
4
|
Tailored Pyridoxal Probes Unravel Novel Cofactor‐Dependent Targets and Antibiotic Hits in Critical Bacterial Pathogens. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202117724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
5
|
Ribič U, Jakše J, Toplak N, Koren S, Kovač M, Klančnik A, Jeršek B. Transporters and Efflux Pumps Are the Main Mechanisms Involved in Staphylococcus epidermidis Adaptation and Tolerance to Didecyldimethylammonium Chloride. Microorganisms 2020; 8:E344. [PMID: 32121333 PMCID: PMC7143832 DOI: 10.3390/microorganisms8030344] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 02/27/2020] [Accepted: 02/28/2020] [Indexed: 01/28/2023] Open
Abstract
Staphylococcus epidermidis cleanroom strains are often exposed to sub-inhibitory concentrations of disinfectants, including didecyldimethylammonium chloride (DDAC). Consequently, they can adapt or even become tolerant to them. RNA-sequencing was used to investigate adaptation and tolerance mechanisms of S. epidermidis cleanroom strains (SE11, SE18), with S. epidermidis SE11Ad adapted and S. epidermidis SE18To tolerant to DDAC. Adaptation to DDAC was identified with up-regulation of genes mainly involved in transport (thioredoxin reductase [pstS], the arsenic efflux pump [gene ID, SE0334], sugar phosphate antiporter [uhpT]), while down-regulation was seen for the Agr system (agrA, arC, agrD, psm, SE1543), for enhanced biofilm formation. Tolerance to DDAC revealed the up-regulation of genes associated with transporters (L-cysteine transport [tcyB]; uracil permease [SE0875]; multidrug transporter [lmrP]; arsenic efflux pump [arsB]); the down-regulation of genes involved in amino-acid biosynthesis (lysine [dapE]; histidine [hisA]; methionine [metC]), and an enzyme involved in peptidoglycan, and therefore cell wall modifications (alanine racemase [SE1079]). We show for the first time the differentially expressed genes in DDAC-adapted and DDAC-tolerant S. epidermidis strains, which highlight the complexity of the responses through the involvement of different mechanisms.
Collapse
Affiliation(s)
- Urška Ribič
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia; (U.R.); (A.K.)
| | - Jernej Jakše
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia;
| | - Nataša Toplak
- Omega d.o.o., Dolinškova 8, SI-1000 Ljubljana, Slovenia; (N.T.); (S.K.); (M.K.)
| | - Simon Koren
- Omega d.o.o., Dolinškova 8, SI-1000 Ljubljana, Slovenia; (N.T.); (S.K.); (M.K.)
| | - Minka Kovač
- Omega d.o.o., Dolinškova 8, SI-1000 Ljubljana, Slovenia; (N.T.); (S.K.); (M.K.)
| | - Anja Klančnik
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia; (U.R.); (A.K.)
| | - Barbara Jeršek
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia; (U.R.); (A.K.)
| |
Collapse
|
6
|
Wang J, Li H, Pan J, Dong J, Zhou X, Niu X, Deng X. Oligopeptide Targeting Sortase A as Potential Anti-infective Therapy for Staphylococcus aureus. Front Microbiol 2018; 9:245. [PMID: 29491861 PMCID: PMC5817083 DOI: 10.3389/fmicb.2018.00245] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 01/31/2018] [Indexed: 01/13/2023] Open
Abstract
Sortase A (SrtA)-catalyzed anchorage of surface proteins in most Gram-positive bacteria is indispensable for their virulence, suggesting that this transpeptidase is a promising target for antivirulence therapy. Here, an oligopeptide, LPRDA, was identified as an effective inhibitor of SrtA via virtual screening based on the LPXTG substrate sequence, and it was found to inhibit SrtA activity in vitro and in vivo (IC50 = 10.61 μM) by competitively occupying the active site of SrtA. Further, the oligopeptide treatment had no anti-Staphylococcus aureus activity, but it provided protection against S. aureus-induced mastitis in a mouse model. These findings indicate that the oligopeptide could be used as an effective anti-infective agent for the treatment of infection caused by S. aureus or other Gram-positive bacteria via the targeting of SrtA.
Collapse
Affiliation(s)
- Jianfeng Wang
- Center of Infection and Immunity, The First Hospital, Jilin University, Changchun, China.,Key Laboratory of Zoonosis, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Hongen Li
- Center of Infection and Immunity, The First Hospital, Jilin University, Changchun, China.,Key Laboratory of Zoonosis, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Juan Pan
- Tianjin International Travel Healthcare Center, Tianjin, China
| | - Jing Dong
- Key Laboratory of Zoonosis, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Xuan Zhou
- Key Laboratory of Zoonosis, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Xiaodi Niu
- Key Laboratory of Zoonosis, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Xuming Deng
- Center of Infection and Immunity, The First Hospital, Jilin University, Changchun, China.,Key Laboratory of Zoonosis, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| |
Collapse
|
7
|
Azam MA, Jayaram U. Induced fit docking, free energy calculation and molecular dynamics studies on Mycobacterium tuberculosis alanine racemase inhibitor. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1393811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Mohammed Afzal Azam
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy (A Constituent College of Jagadguru Sri Shivarathreeswara University, Mysuru) Udhagamandalam, India
| | - Unni Jayaram
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy (A Constituent College of Jagadguru Sri Shivarathreeswara University, Mysuru) Udhagamandalam, India
| |
Collapse
|
8
|
Wang Y, Yang C, Xue W, Zhang T, Liu X, Ju J, Zhao B, Liu D. Selection and characterization of alanine racemase inhibitors against Aeromonas hydrophila. BMC Microbiol 2017; 17:122. [PMID: 28545531 PMCID: PMC5445283 DOI: 10.1186/s12866-017-1010-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 04/13/2017] [Indexed: 02/02/2023] Open
Abstract
Background Combining experimental and computational screening methods has been of keen interest in drug discovery. In the present study, we developed an efficient screening method that has been used to screen 2100 small-molecule compounds for alanine racemase Alr-2 inhibitors. Results We identified ten novel non-substrate Alr-2 inhibitors, of which patulin, homogentisic acid, and hydroquinone were active against Aeromonas hydrophila. The compounds were found to be capable of inhibiting Alr-2 to different extents with 50% inhibitory concentrations (IC50) ranging from 6.6 to 17.7 μM. These compounds inhibited the growth of A. hydrophila with minimal inhibitory concentrations (MICs) ranging from 20 to 120 μg/ml. These compounds have no activity on horseradish peroxidase and d-amino acid oxidase at a concentration of 50 μM. The MTT assay revealed that homogentisic acid and hydroquinone have minimal cytotoxicity against mammalian cells. The kinetic studies indicated a competitive inhibition of homogentisic acid against Alr-2 with an inhibition constant (Ki) of 51.7 μM, while hydroquinone was a noncompetitive inhibitor with a Ki of 212 μM. Molecular docking studies suggested that homogentisic acid binds to the active site of racemase, while hydroquinone lies near the active center of alanine racemase. Conclusions Our findings suggested that combining experimental and computational methods could be used for an efficient, large-scale screening of alanine racemase inhibitors against A. hydrophila that could be applied in the development of new antibiotics against A. hydrophila. Electronic supplementary material The online version of this article (doi:10.1186/s12866-017-1010-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Yaping Wang
- College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Chao Yang
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Wen Xue
- College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Ting Zhang
- College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Xipei Liu
- College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Jiansong Ju
- College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Baohua Zhao
- College of Life Science, Hebei Normal University, Shijiazhuang, China.
| | - Dong Liu
- College of Life Science, Hebei Normal University, Shijiazhuang, China.
| |
Collapse
|
9
|
Sharma V, Wang YS, Liu WR. Probing the Catalytic Charge-Relay System in Alanine Racemase with Genetically Encoded Histidine Mimetics. ACS Chem Biol 2016; 11:3305-3309. [PMID: 27978711 DOI: 10.1021/acschembio.6b00940] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Histidine is a unique amino acid with an imidazole side chain in which both of the nitrogen atoms are capable of serving as a proton donor and proton acceptor in hydrogen bonding interactions. In order to probe the functional role of histidine involved in hydrogen bonding networks, fine-tuning the hydrogen bonding potential of the imidazole side chain is required but not feasible through traditional mutagenesis methods. Here, we show that two close mimetics of histidine, 3-methyl-histidine and thiazole alanine, can be genetically encoded using engineered pyrrolysine incorporation machinery. Replacement of the three histidine residues predicted to be involved in an extended charge-relay system in alanine racemase with 3-methyl-histidine or thiazole alanine shows a dramatic loss in the enzyme's catalytic efficiency, implying the role of this extended charge-relay system in activating the active site residue Y265, a general acid/base catalyst in the enzyme.
Collapse
Affiliation(s)
- Vangmayee Sharma
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Yane-Shih Wang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Wenshe R. Liu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| |
Collapse
|
10
|
Soo VWC, Yosaatmadja Y, Squire CJ, Patrick WM. Mechanistic and Evolutionary Insights from the Reciprocal Promiscuity of Two Pyridoxal Phosphate-dependent Enzymes. J Biol Chem 2016; 291:19873-87. [PMID: 27474741 PMCID: PMC5025676 DOI: 10.1074/jbc.m116.739557] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Indexed: 11/06/2022] Open
Abstract
Enzymes that utilize the cofactor pyridoxal 5′-phosphate play essential roles in amino acid metabolism in all organisms. The cofactor is used by proteins that adopt at least five different folds, which raises questions about the evolutionary processes that might explain the observed distribution of functions among folds. In this study, we show that a representative of fold type III, the Escherichia coli alanine racemase (ALR), is a promiscuous cystathionine β-lyase (CBL). Furthermore, E. coli CBL (fold type I) is a promiscuous alanine racemase. A single round of error-prone PCR and selection yielded variant ALR(Y274F), which catalyzes cystathionine β-elimination with a near-native Michaelis constant (Km = 3.3 mm) but a poor turnover number (kcat ≈10 h−1). In contrast, directed evolution also yielded CBL(P113S), which catalyzes l-alanine racemization with a poor Km (58 mm) but a high kcat (22 s−1). The structures of both variants were solved in the presence and absence of the l-alanine analogue, (R)-1-aminoethylphosphonic acid. As expected, the ALR active site was enlarged by the Y274F substitution, allowing better access for cystathionine. More surprisingly, the favorable kinetic parameters of CBL(P113S) appear to result from optimizing the pKa of Tyr-111, which acts as the catalytic acid during l-alanine racemization. Our data emphasize the short mutational routes between the functions of pyridoxal 5′-phosphate-dependent enzymes, regardless of whether or not they share the same fold. Thus, they confound the prevailing model of enzyme evolution, which predicts that overlapping patterns of promiscuity result from sharing a common multifunctional ancestor.
Collapse
Affiliation(s)
- Valerie W C Soo
- From the Institute of Natural and Mathematical Sciences, Massey University, Auckland 0632
| | - Yuliana Yosaatmadja
- the School of Biological Sciences, University of Auckland, Auckland 1142, and
| | | | - Wayne M Patrick
- the Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand
| |
Collapse
|
11
|
Affiliation(s)
- Mohammed Afzal Azam
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, Udhagamandalam, Tamil Nadu, India
| | - Unni Jayaram
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, Udhagamandalam, Tamil Nadu, India
| |
Collapse
|
12
|
Liu D, Liu X, Zhang L, Jiao H, Ju J, Zhao B. Biochemical characteristics of an alanine racemase from Aeromonas hydrophil HBNUAh01. Microbiology (Reading) 2015. [DOI: 10.1134/s0026261715020071] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
|
13
|
Lee Y, Mootien S, Shoen C, Destefano M, Cirillo P, Asojo OA, Yeung KR, Ledizet M, Cynamon MH, Aristoff PA, Koski RA, Kaplan PA, Anthony KG. Inhibition of mycobacterial alanine racemase activity and growth by thiadiazolidinones. Biochem Pharmacol 2013; 86:222-30. [PMID: 23680030 DOI: 10.1016/j.bcp.2013.05.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 05/02/2013] [Accepted: 05/03/2013] [Indexed: 11/25/2022]
Abstract
The genus Mycobacterium includes non-pathogenic species such as M. smegmatis, and pathogenic species such as M. tuberculosis, the causative agent of tuberculosis (TB). Treatment of TB requires a lengthy regimen of several antibiotics, whose effectiveness has been compromised by the emergence of resistant strains. New antibiotics that can shorten the treatment course and those that have not been compromised by bacterial resistance are needed. In this study, we report that thiadiazolidinones, a relatively little-studied heterocyclic class, inhibit the activity of mycobacterial alanine racemase, an essential enzyme that converts l-alanine to d-alanine for peptidoglycan synthesis. Twelve members of the thiadiazolidinone family were evaluated for inhibition of M. tuberculosis and M. smegmatis alanine racemase activity and bacterial growth. Thiadiazolidinones inhibited M. tuberculosis and M. smegmatis alanine racemases to different extents with 50% inhibitory concentrations (IC50) ranging from <0.03 to 28μM and 23 to >150μM, respectively. The compounds also inhibited the growth of these bacteria, including multidrug resistant strains of M. tuberculosis. The minimal inhibitory concentrations (MIC) for drug-susceptible M. tuberculosis and M. smegmatis ranged from 6.25μg/ml to 100μg/ml, and from 1.56 to 6.25μg/ml for drug-resistant M. tuberculosis. The in vitro activities of thiadiazolidinones suggest that this family of compounds might represent starting points for medicinal chemistry efforts aimed at developing novel antimycobacterial agents.
Collapse
Affiliation(s)
- Yashang Lee
- L2 Diagnostics LLC, 300 George St., New Haven, CT 06511, USA
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Munier-Lehmann H, Vidalain PO, Tangy F, Janin YL. On dihydroorotate dehydrogenases and their inhibitors and uses. J Med Chem 2013; 56:3148-67. [PMID: 23452331 DOI: 10.1021/jm301848w] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Proper nucleosides availability is crucial for the proliferation of living entities (eukaryotic cells, parasites, bacteria, and virus). Accordingly, the uses of inhibitors of the de novo nucleosides biosynthetic pathways have been investigated in the past. In the following we have focused on dihydroorotate dehydrogenase (DHODH), the fourth enzyme in the de novo pyrimidine nucleosides biosynthetic pathway. We first described the different types of enzyme in terms of sequence, structure, and biochemistry, including the reported bioassays. In a second part, the series of inhibitors of this enzyme along with a description of their potential or actual uses were reviewed. These inhibitors are indeed used in medicine to treat autoimmune diseases such as rheumatoid arthritis or multiple sclerosis (leflunomide and teriflunomide) and have been investigated in treatments of cancer, virus, and parasite infections (i.e., malaria) as well as in crop science.
Collapse
Affiliation(s)
- Hélène Munier-Lehmann
- Institut Pasteur, Unité de Chimie et Biocatalyse, Département de Biologie Structurale et Chimie, 28 Rue du Dr. Roux, 75724 Paris Cedex 15, France
| | | | | | | |
Collapse
|
15
|
Prosser GA, de Carvalho LPS. Kinetic mechanism and inhibition of Mycobacterium tuberculosis D-alanine:D-alanine ligase by the antibiotic D-cycloserine. FEBS J 2013; 280:1150-66. [PMID: 23286234 DOI: 10.1111/febs.12108] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 12/17/2012] [Accepted: 12/19/2012] [Indexed: 11/30/2022]
Abstract
D-cycloserine (DCS) is an antibiotic that is currently used in second-line treatment of tuberculosis. DCS is a structural analogue of D-alanine, and targets two enzymes involved in the cytosolic stages of peptidoglycan synthesis: alanine racemase (Alr) and D-alanine:D-alanine ligase (Ddl). The mechanisms of inhibition of DCS have been well-assessed using Alr and Ddl enzymes from various bacterial species, but little is known regarding the interactions of DCS with the mycobacterial orthologues of these enzymes. We have over-expressed and purified recombinant Mycobacterium tuberculosis Ddl (MtDdl; Rv2981c), and report a kinetic examination of the enzyme with both its native substrate and DCS. MtDdl is activated by K(+), follows an ordered ter ter mechanism and displays distinct affinities for D-Ala at each D-Ala binding site (K(m,D-Ala1) = 0.075 mm, K(m,D-Ala2) = 3.6 mm). ATP is the first substrate to bind and is necessary for subsequent binding of D-alanine or DCS. The pH dependence of MtDdl kinetic parameters indicate that general base chemistry is involved in the catalytic step. DCS was found to competitively inhibit D-Ala binding at both MtDdl D-Ala sites with equal affinity (K(i,DCS1) = 14 μm, K(i,DCS2) = 25 μm); however, each enzyme active site can only accommodate a single DCS molecule at a given time. The pH dependence of K(i,DCS2) revealed a loss of DCS binding affinity at high pH (pK(a) = 7.5), suggesting that DCS binds optimally in the zwitterionic form. The results of this study may assist in the design and development of novel Ddl-specific inhibitors for use as anti-mycobacterial agents.
Collapse
Affiliation(s)
- Gareth A Prosser
- Mycobacterial Research Division, Medical Research Council National Institute for Medical Research, London, UK
| | | |
Collapse
|