1
|
Qin Y, Teng Y, Yang Y, Mao Z, Zhao S, Zhang N, Li X, Niu W. Advancements in inhibitors of crucial enzymes in the cysteine biosynthetic pathway: Serine acetyltransferase and O-acetylserine sulfhydrylase. Chem Biol Drug Des 2024; 104:e14573. [PMID: 38965664 DOI: 10.1111/cbdd.14573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 05/17/2024] [Accepted: 06/18/2024] [Indexed: 07/06/2024]
Abstract
Infectious diseases have been jeopardized problem that threaten public health over a long period of time. The growing prevalence of drug-resistant pathogens and infectious cases have led to a decrease in the number of effective antibiotics, which highlights the urgent need for the development of new antibacterial agents. Serine acetyltransferase (SAT), also known as CysE in certain bacterial species, and O-acetylserine sulfhydrylase (OASS), also known as CysK in select bacteria, are indispensable enzymes within the cysteine biosynthesis pathway of various pathogenic microorganisms. These enzymes play a crucial role in the survival of these pathogens, making SAT and OASS promising targets for the development of novel anti-infective agents. In this comprehensive review, we present an introduction to the structure and function of SAT and OASS, along with an overview of existing inhibitors for SAT and OASS as potential antibacterial agents. Our primary focus is on elucidating the inhibitory activities, structure-activity relationships, and mechanisms of action of these inhibitors. Through this exploration, we aim to provide insights into promising strategies and prospects in the development of antibacterial agents that target these essential enzymes.
Collapse
Affiliation(s)
- Yinhui Qin
- Department of Pharmacy, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, Henan, China
| | - Yuetai Teng
- Department of Pharmacy, Jinan Vocational College of Nursing, Jinan, China
| | - Yan Yang
- Department of Pharmacy, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, Henan, China
| | - Zhenkun Mao
- Department of Pharmacy, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, Henan, China
| | - Shengyu Zhao
- Shenyang Pharmaceutical University, Shenyang, China
| | - Na Zhang
- Shandong Academy of Chinese Medicine, Jinan, China
| | - Xu Li
- Institute of Chemistry Henan Academy of Sciences, Zhengzhou, Henan, China
| | - Weihong Niu
- Department of Pathology, Henan Key Laboratory for Digital Pathology Medicine, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, Henan, China
| |
Collapse
|
2
|
Tao Y, Zheng D, Zou W, Guo T, Liao G, Zhou W. Targeting the cysteine biosynthesis pathway in microorganisms: Mechanism, structure, and drug discovery. Eur J Med Chem 2024; 271:116461. [PMID: 38691891 DOI: 10.1016/j.ejmech.2024.116461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/16/2024] [Accepted: 04/27/2024] [Indexed: 05/03/2024]
Abstract
Owing to the global health crisis of resistant pathogenic infections, researchers are emphasizing the importance of novel prevention and control strategies. Existing antimicrobial drugs predominantly target a few pathways, and their widespread use has pervasively increased drug resistance. Therefore, it is imperative to develop new antimicrobial drugs with novel targets and chemical structures. The de novo cysteine biosynthesis pathway, one of the microbial metabolic pathways, plays a crucial role in pathogenicity and drug resistance. This pathway notably differs from that in humans, thereby representing an unexplored target for developing antimicrobial drugs. Herein, we have presented an overview of cysteine biosynthesis pathways and their roles in the pathogenicity of various microorganisms. Additionally, we have investigated the structure and function of enzymes involved in these pathways as well as have discussed drug design strategies and structure-activity relationships of the enzyme inhibitors. This review provides valuable insights for developing novel antimicrobials and offers new avenues to combat drug resistance.
Collapse
Affiliation(s)
- Ying Tao
- State Key Laboratory of Resource Insects, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China
| | - Dandan Zheng
- State Key Laboratory of Resource Insects, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China
| | - Wei Zou
- State Key Laboratory of Resource Insects, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China
| | - Ting Guo
- State Key Laboratory of Resource Insects, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China
| | - Guojian Liao
- State Key Laboratory of Resource Insects, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China.
| | - Wei Zhou
- State Key Laboratory of Resource Insects, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China.
| |
Collapse
|
3
|
Foletto-Felipe MDP, Abrahão J, Siqueira-Soares RDC, Contesoto IDC, Grizza LHE, de Almeida GHG, Constantin RP, Philippsen GS, Seixas FAV, Bueno PSA, de Oliveira MAS, Constantin RP, Dos Santos WD, Ferrarese-Filho O, Marchiosi R. Inhibition of O-acetylserine (thiol) lyase as a promising new mechanism of action for herbicides. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 204:108127. [PMID: 37890229 DOI: 10.1016/j.plaphy.2023.108127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/13/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023]
Abstract
Enzymes of the sulfur assimilation pathway of plants have been identified as potential targets for herbicide development, given their crucial role in synthesizing amino acids, coenzymes, and various sulfated compounds. In this pathway, O-acetylserine (thiol) lyase (OAS-TL; EC 2.5.1.47) catalyzes the synthesis of L-cysteine through the incorporation of sulfate into O-acetylserine (OAS). This study used an in silico approach to select seven inhibitors for OAS-TL. The in silico experiments revealed that S-benzyl-L-cysteine (SBC) had a better docking score (-7.0 kcal mol-1) than the substrate OAS (-6.6 kcal mol-1), indicating its suitable interaction with the active site of the enzyme. In vitro experiments showed that SBC is a non-competitive inhibitor of OAS-TL from Arabidopsis thaliana expressed heterologously in Escherichia coli, with a Kic of 4.29 mM and a Kiu of 5.12 mM. When added to the nutrient solution, SBC inhibited the growth of maize and morning glory weed plants due to the reduction of L-cysteine synthesis. Remarkably, morning glory was more sensitive than maize. As proof of its mechanism of action, L-cysteine supplementation to the nutrient solution mitigated the inhibitory effect of SBC on the growth of morning glory. Taken together, our data suggest that reduced L-cysteine synthesis is the primary cause of growth inhibition in maize and morning glory plants exposed to SBC. Furthermore, our findings indicate that inhibiting OAS-TL could potentially be a novel approach for herbicidal action.
Collapse
Affiliation(s)
- Marcela de Paiva Foletto-Felipe
- Laboratory of Plant Biochemistry, Department of Biochemistry, State University of Maringá, Paraná, Brazil; Coordination of Degree in Biological Sciences, Federal Technological University of Paraná, Campus Dois Vizinhos, Paraná, Brazil
| | - Josielle Abrahão
- Laboratory of Plant Biochemistry, Department of Biochemistry, State University of Maringá, Paraná, Brazil
| | | | | | | | | | - Renato Polimeni Constantin
- Laboratory of Plant Biochemistry, Department of Biochemistry, State University of Maringá, Paraná, Brazil
| | | | | | | | | | | | | | - Osvaldo Ferrarese-Filho
- Laboratory of Plant Biochemistry, Department of Biochemistry, State University of Maringá, Paraná, Brazil
| | - Rogério Marchiosi
- Laboratory of Plant Biochemistry, Department of Biochemistry, State University of Maringá, Paraná, Brazil.
| |
Collapse
|
4
|
Abd El-Aleam RH, George RF, Georgey HH, Abdel-Rahman HM. Bacterial virulence factors: a target for heterocyclic compounds to combat bacterial resistance. RSC Adv 2021; 11:36459-36482. [PMID: 35494393 PMCID: PMC9043591 DOI: 10.1039/d1ra06238g] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/01/2021] [Indexed: 12/17/2022] Open
Abstract
Antibiotic resistance is one of the most important challenges of the 21st century. However, the growing understanding of bacterial pathogenesis and cell-to-cell communication has revealed many potential strategies for the discovery of drugs that can be used for the treatment of bacterial infections. Interfering with bacterial virulence and/or quorum sensing could be a particularly interesting approach, because it is believed to exert less selective pressure on the bacterial resistance than with traditional strategies, geared toward killing bacteria or preventing their growth. Here, we discuss the mechanism of bacterial virulence, presenting promising strategies and recently synthesized heterocyclic compounds to combat future bacterial infections.
Collapse
Affiliation(s)
- Rehab H Abd El-Aleam
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Modern University for Technology and Information MTI Cairo 11571 Egypt
| | - Riham F George
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University Cairo 11562 Egypt
| | - Hanan H Georgey
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University Cairo 11562 Egypt
- Pharmaceutical Chemistry Department, Faculty of Pharmacy and Drug Technology, Egyptian Chinese University Cairo 11786 Egypt
| | - Hamdy M Abdel-Rahman
- Medicinal Chemistry Department, Faculty of Pharmacy, Assiut University Assiut 71526 Egypt
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Nahda University Beni Suef Egypt
| |
Collapse
|
5
|
A Competitive O-Acetylserine Sulfhydrylase Inhibitor Modulates the Formation of Cysteine Synthase Complex. Catalysts 2021. [DOI: 10.3390/catal11060700] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Cysteine is the main precursor of sulfur-containing biological molecules in bacteria and contributes to the control of the cell redox state. Hence, this amino acid plays an essential role in microbial survival and pathogenicity and the reductive sulfate assimilation pathway is considered a promising target for the development of new antibacterials. Serine acetyltransferase (SAT) and O-acetylserine sulfhydrylase (OASS-A), the enzymes catalyzing the last two steps of cysteine biosynthesis, engage in the formation of the cysteine synthase (CS) complex. The interaction between SAT and OASS-A finely tunes cysteine homeostasis, and the development of inhibitors targeting either protein–protein interaction or the single enzymes represents an attractive strategy to undermine bacterial viability. Given the peculiar mode of interaction between SAT and OASS-A, which exploits the insertion of SAT C-terminal sequence into OASS-A active site, we tested whether a recently developed competitive inhibitor of OASS-A exhibited any effect on the CS stability. Through surface plasmon resonance spectroscopy, we (i) determined the equilibrium constant for the Salmonella Typhimurium CS complex formation and (ii) demonstrated that the inhibitor targeting OASS-A active site affects CS complex formation. For comparison, the Escherichia coli CS complex was also investigated, with the aim of testing the potential broad-spectrum activity of the candidate antimicrobial compound.
Collapse
|
6
|
Magalhães J, Franko N, Raboni S, Annunziato G, Tammela P, Bruno A, Bettati S, Armao S, Spadini C, Cabassi CS, Mozzarelli A, Pieroni M, Campanini B, Costantino G. Discovery of Substituted (2-Aminooxazol-4-yl)Isoxazole-3-carboxylic Acids as Inhibitors of Bacterial Serine Acetyltransferase in the Quest for Novel Potential Antibacterial Adjuvants. Pharmaceuticals (Basel) 2021; 14:ph14020174. [PMID: 33672408 PMCID: PMC7931047 DOI: 10.3390/ph14020174] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/15/2021] [Accepted: 02/19/2021] [Indexed: 02/07/2023] Open
Abstract
Many bacteria and actinomycetales use L-cysteine biosynthesis to increase their tolerance to antibacterial treatment and establish a long-lasting infection. In turn, this might lead to the onset of antimicrobial resistance that currently represents one of the most menacing threats to public health worldwide. The biosynthetic machinery required to synthesise L-cysteine is absent in mammals; therefore, its exploitation as a drug target is particularly promising. In this article, we report a series of inhibitors of Salmonella thyphimurium serine acetyltransferase (SAT), the enzyme that catalyzes the rate-limiting step of L-cysteine biosynthesis. The development of such inhibitors started with the virtual screening of an in-house library of compounds that led to the selection of seven structurally unrelated hit derivatives. A set of molecules structurally related to hit compound 5, coming either from the original library or from medicinal chemistry efforts, were tested to determine a preliminary structure–activity relationship and, especially, to improve the inhibitory potency of the derivatives, that was indeed ameliorated by several folds compared to hit compound 5 Despite these progresses, at this stage, the most promising compound failed to interfere with bacterial growth when tested on a Gram-negative model organism, anticipating the need for further research efforts.
Collapse
Affiliation(s)
- Joana Magalhães
- P4T Group, Department of Food and Drug, University of Parma, 43124 Parma, Italy; (J.M.); (G.A.); (A.B.); (G.C.)
| | - Nina Franko
- Laboratory of Biochemistry and Molecular Biology, Department of Food and Drug, University of Parma, 43124 Parma, Italy; (N.F.); (S.R.); (S.A.); (A.M.); (B.C.)
| | - Samanta Raboni
- Laboratory of Biochemistry and Molecular Biology, Department of Food and Drug, University of Parma, 43124 Parma, Italy; (N.F.); (S.R.); (S.A.); (A.M.); (B.C.)
- Institute of Biophysics, CNR, 56124 Pisa, Italy;
| | - Giannamaria Annunziato
- P4T Group, Department of Food and Drug, University of Parma, 43124 Parma, Italy; (J.M.); (G.A.); (A.B.); (G.C.)
- Centro Interdipartimentale Misure (CIM) ‘G. Casnati’, University of Parma, 43124 Parma, Italy
| | - Päivi Tammela
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), FI-00014 Helsinki, Finland;
| | - Agostino Bruno
- P4T Group, Department of Food and Drug, University of Parma, 43124 Parma, Italy; (J.M.); (G.A.); (A.B.); (G.C.)
| | - Stefano Bettati
- Institute of Biophysics, CNR, 56124 Pisa, Italy;
- Department of Medicine and Surgery, University of Parma, Via Volturno, 39, 43125 Parma, Italy
- National Institute of Biostructures and Biosystems, 00136 Rome, Italy
| | - Stefano Armao
- Laboratory of Biochemistry and Molecular Biology, Department of Food and Drug, University of Parma, 43124 Parma, Italy; (N.F.); (S.R.); (S.A.); (A.M.); (B.C.)
| | - Costanza Spadini
- Operative Unit of Animals Infectious Diseases, Department of Veterinary Science, University of Parma, Via del Taglio 10, 43126 Parma, Italy; (C.S.); (C.S.C.)
| | - Clotilde Silvia Cabassi
- Operative Unit of Animals Infectious Diseases, Department of Veterinary Science, University of Parma, Via del Taglio 10, 43126 Parma, Italy; (C.S.); (C.S.C.)
| | - Andrea Mozzarelli
- Laboratory of Biochemistry and Molecular Biology, Department of Food and Drug, University of Parma, 43124 Parma, Italy; (N.F.); (S.R.); (S.A.); (A.M.); (B.C.)
- Institute of Biophysics, CNR, 56124 Pisa, Italy;
- National Institute of Biostructures and Biosystems, 00136 Rome, Italy
| | - Marco Pieroni
- P4T Group, Department of Food and Drug, University of Parma, 43124 Parma, Italy; (J.M.); (G.A.); (A.B.); (G.C.)
- Centro Interdipartimentale Misure (CIM) ‘G. Casnati’, University of Parma, 43124 Parma, Italy
- Correspondence: ; Tel.: +39-0521-905054
| | - Barbara Campanini
- Laboratory of Biochemistry and Molecular Biology, Department of Food and Drug, University of Parma, 43124 Parma, Italy; (N.F.); (S.R.); (S.A.); (A.M.); (B.C.)
| | - Gabriele Costantino
- P4T Group, Department of Food and Drug, University of Parma, 43124 Parma, Italy; (J.M.); (G.A.); (A.B.); (G.C.)
- Centro Interdipartimentale Misure (CIM) ‘G. Casnati’, University of Parma, 43124 Parma, Italy
| |
Collapse
|
7
|
Annunziato G, Spadini C, Franko N, Storici P, Demitri N, Pieroni M, Flisi S, Rosati L, Iannarelli M, Marchetti M, Magalhaes J, Bettati S, Mozzarelli A, Cabassi CS, Campanini B, Costantino G. Investigational Studies on a Hit Compound Cyclopropane-Carboxylic Acid Derivative Targeting O-Acetylserine Sulfhydrylase as a Colistin Adjuvant. ACS Infect Dis 2021; 7:281-292. [PMID: 33513010 DOI: 10.1021/acsinfecdis.0c00378] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Antibacterial adjuvants are of great significance, since they allow the therapeutic dose of conventional antibiotics to be lowered and reduce the insurgence of antibiotic resistance. Herein, we report that an O-acetylserine sulfhydrylase (OASS) inhibitor can be used as a colistin adjuvant to treat infections caused by Gram-positive and Gram-negative pathogens. A compound that binds OASS with a nM dissociation constant was tested as an adjuvant of colistin against six critical pathogens responsible for infections spreading worldwide, Escherichia coli, Salmonella enterica serovar Typhimurium, Klebisiella pneumoniae, Staphylococcus aureus, methicillin-resistant Staphylococcus aureus, and Staphylococcus pseudintermedius. The compound showed promising synergistic or additive activities against all of them. Knockout experiments confirmed the intracellular target engagement supporting the proposed mechanism of action. Moreover, compound toxicity was evaluated by means of its hemolytic activity against sheep defibrinated blood cells, showing a good safety profile. The 3D structure of the compound in complex with OASS was determined at 1.2 Å resolution by macromolecular crystallography, providing for the first time structural insights about the nature of the interaction between the enzyme and this class of competitive inhibitors. Our results provide a robust proof of principle supporting OASS as a potential nonessential antibacterial target to develop a new class of adjuvants and the structural basis for further structure-activity relationship studies.
Collapse
Affiliation(s)
- Giannamaria Annunziato
- P4T Group, Department of Food and Drugs, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Costanza Spadini
- Operative Unit of Animals Infectious Diseases, Department of Veterinary Science, University of Parma, via del Taglio, 8, 43126 Parma, Italy
| | - Nina Franko
- Laboratory of Biochemistry and Molecular Biology, Department of Food and Drugs, University of Parma, via Parco Area delle Scienze 23/A, 43124 Parma, Italy
| | - Paola Storici
- Elettra - Sincrotrone Trieste S.C.p.A., SS 14
- km 163,5 in AREA Science Park, 34149 Trieste, Italy
| | - Nicola Demitri
- Elettra - Sincrotrone Trieste S.C.p.A., SS 14
- km 163,5 in AREA Science Park, 34149 Trieste, Italy
| | - Marco Pieroni
- P4T Group, Department of Food and Drugs, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Sara Flisi
- Operative Unit of Animals Infectious Diseases, Department of Veterinary Science, University of Parma, via del Taglio, 8, 43126 Parma, Italy
| | - Lucrezia Rosati
- Operative Unit of Animals Infectious Diseases, Department of Veterinary Science, University of Parma, via del Taglio, 8, 43126 Parma, Italy
| | - Mattia Iannarelli
- Operative Unit of Animals Infectious Diseases, Department of Veterinary Science, University of Parma, via del Taglio, 8, 43126 Parma, Italy
| | - Marialaura Marchetti
- Biopharmanet-TEC Interdepartmental Center, University of Parma, 43124 Parma, Italy
| | - Joana Magalhaes
- P4T Group, Department of Food and Drugs, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Stefano Bettati
- Department of Medicine and Surgery, University of Parma, via Volturno, 39, 43125 Parma, Italy
- Biopharmanet-TEC Interdepartmental Center, University of Parma, 43124 Parma, Italy
- Institute of Biophysics, CNR, 56124 Pisa, Italy
| | - Andrea Mozzarelli
- Laboratory of Biochemistry and Molecular Biology, Department of Food and Drugs, University of Parma, via Parco Area delle Scienze 23/A, 43124 Parma, Italy
- Biopharmanet-TEC Interdepartmental Center, University of Parma, 43124 Parma, Italy
- Institute of Biophysics, CNR, 56124 Pisa, Italy
| | - Clotilde Silvia Cabassi
- Operative Unit of Animals Infectious Diseases, Department of Veterinary Science, University of Parma, via del Taglio, 8, 43126 Parma, Italy
| | - Barbara Campanini
- Laboratory of Biochemistry and Molecular Biology, Department of Food and Drugs, University of Parma, via Parco Area delle Scienze 23/A, 43124 Parma, Italy
- Biopharmanet-TEC Interdepartmental Center, University of Parma, 43124 Parma, Italy
| | - Gabriele Costantino
- P4T Group, Department of Food and Drugs, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| |
Collapse
|
8
|
Wallace MJ, Dharuman S, Fernando DM, Reeve SM, Gee CT, Yao J, Griffith EC, Phelps GA, Wright WC, Elmore JM, Lee RB, Chen T, Lee RE. Discovery and Characterization of the Antimetabolite Action of Thioacetamide-Linked 1,2,3-Triazoles as Disruptors of Cysteine Biosynthesis in Gram-Negative Bacteria. ACS Infect Dis 2020; 6:467-478. [PMID: 31887254 DOI: 10.1021/acsinfecdis.9b00406] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Increasing rates of drug-resistant Gram-negative (GN) infections, combined with a lack of new GN-effective antibiotic classes, are driving the need for the discovery of new agents. Bacterial metabolism represents an underutilized mechanism of action in current antimicrobial therapies. Therefore, we sought to identify novel antimetabolites that disrupt key metabolic pathways and explore the specific impacts of these agents on bacterial metabolism. This study describes the successful application of this approach to discover a new series of chemical probes, N-(phenyl)thioacetamide-linked 1,2,3-triazoles (TAT), that target cysteine synthase A (CysK), an enzyme unique to bacteria that is positioned at a key juncture between several fundamental pathways. The TAT class was identified using a high-throughput screen against Escherichia coli designed to identify modulators of pathways related to folate biosynthesis. TAT analog synthesis demonstrated a clear structure-activity relationship, and activity was confirmed against GN antifolate-resistant clinical isolates. Spontaneous TAT resistance mutations were tracked to CysK, and mode of action studies led to the identification of a false product formation mechanism between the CysK substrate O-acetyl-l-serine and the TATs. Global transcriptional responses to TAT treatment revealed that these antimetabolites impose substantial disruption of key metabolic networks beyond cysteine biosynthesis. This study highlights the potential of antimetabolite drug discovery as a promising approach to the discovery of novel GN antibiotics and the pharmacological promise of TAT CysK probes.
Collapse
Affiliation(s)
- Miranda J. Wallace
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
- Department of Microbiology, Immunology, and Biochemistry, The University of Tennessee Health Science Center, 858 Madison Avenue, Memphis, Tennessee 38163, United States
| | - Suresh Dharuman
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Dinesh M. Fernando
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Stephanie M. Reeve
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Clifford T. Gee
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Jiangwei Yao
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Elizabeth C. Griffith
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Gregory A. Phelps
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - William C. Wright
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - John M. Elmore
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Robin B. Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Richard E. Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| |
Collapse
|
9
|
Annunziato G. Strategies to Overcome Antimicrobial Resistance (AMR) Making Use of Non-Essential Target Inhibitors: A Review. Int J Mol Sci 2019; 20:E5844. [PMID: 31766441 PMCID: PMC6928725 DOI: 10.3390/ijms20235844] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 12/23/2022] Open
Abstract
Antibiotics have always been considered as one of the most relevant discoveries of the twentieth century. Unfortunately, the dawn of the antibiotic era has sadly corresponded to the rise of the phenomenon of antimicrobial resistance (AMR), which is a natural process whereby microbes evolve in such a way to withstand the action of drugs. In this context, the identification of new potential antimicrobial targets and/or the identification of new chemical entities as antimicrobial drugs are in great demand. To date, among the many possible approaches used to deal with antibiotic resistance is the use of antibiotic adjuvants that hit bacterial non-essential targets. In this review, the author focuses on the discovery of antibiotic adjuvants and on new tools to study and reduce the prevalence of resistant bacterial infections.
Collapse
Affiliation(s)
- Giannamaria Annunziato
- Probes for Targets Group (P4T group), Department of food and Drug, University of Parma, 43124 Parma, Italy
| |
Collapse
|
10
|
Combination of SAXS and Protein Painting Discloses the Three-Dimensional Organization of the Bacterial Cysteine Synthase Complex, a Potential Target for Enhancers of Antibiotic Action. Int J Mol Sci 2019; 20:ijms20205219. [PMID: 31640223 PMCID: PMC6829319 DOI: 10.3390/ijms20205219] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 09/10/2019] [Accepted: 09/17/2019] [Indexed: 01/03/2023] Open
Abstract
The formation of multienzymatic complexes allows for the fine tuning of many aspects of enzymatic functions, such as efficiency, localization, stability, and moonlighting. Here, we investigated, in solution, the structure of bacterial cysteine synthase (CS) complex. CS is formed by serine acetyltransferase (CysE) and O-acetylserine sulfhydrylase isozyme A (CysK), the enzymes that catalyze the last two steps of cysteine biosynthesis in bacteria. CysK and CysE have been proposed as potential targets for antibiotics, since cysteine and related metabolites are intimately linked to protection of bacterial cells against redox damage and to antibiotic resistance. We applied a combined approach of small-angle X-ray scattering (SAXS) spectroscopy and protein painting to obtain a model for the solution structure of CS. Protein painting allowed the identification of protein–protein interaction hotspots that were then used as constrains to model the CS quaternary assembly inside the SAXS envelope. We demonstrate that the active site entrance of CysK is involved in complex formation, as suggested by site-directed mutagenesis and functional studies. Furthermore, complex formation involves a conformational change in one CysK subunit that is likely transmitted through the dimer interface to the other subunit, with a regulatory effect. Finally, SAXS data indicate that only one active site of CysK is involved in direct interaction with CysE and unambiguously unveil the quaternary arrangement of CS.
Collapse
|
11
|
Pang H, Wu D, Cong H, Yin G. Stereoselective Palladium-Catalyzed 1,3-Arylboration of Unconjugated Dienes for Expedient Synthesis of 1,3-Disubstituted Cyclohexanes. ACS Catal 2019. [DOI: 10.1021/acscatal.9b02747] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Hailiang Pang
- The Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Dong Wu
- The Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Hengjiang Cong
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Guoyin Yin
- The Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| |
Collapse
|
12
|
Lensmire JM, Hammer ND. Nutrient sulfur acquisition strategies employed by bacterial pathogens. Curr Opin Microbiol 2019; 47:52-58. [DOI: 10.1016/j.mib.2018.11.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 11/04/2018] [Accepted: 11/07/2018] [Indexed: 10/27/2022]
|
13
|
Insights into multifaceted activities of CysK for therapeutic interventions. 3 Biotech 2019; 9:44. [PMID: 30675454 DOI: 10.1007/s13205-019-1572-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 01/10/2019] [Indexed: 01/24/2023] Open
Abstract
CysK (O-acetylserine sulfhydrylase) is a pyridoxal-5' phosphate-dependent enzyme which catalyzes the second step of the de novo cysteine biosynthesis pathway by converting O-acetyl serine (OAS) into l-cysteine in the presence of sulfide. The first step of the cysteine biosynthesis involves formation of OAS from serine and acetyl CoA by CysE (serine acetyltransferase). Apart from role of CysK in cysteine biosynthesis, recent studies have revealed various additional roles of this enzyme in bacterial physiology. Other than the suggested regulatory role in cysteine production, other activities of CysK include involvement of CysK-in contact-dependent toxin activation in Gram-negative pathogens, as a transcriptional regulator of CymR by stabilizing the CymR-DNA interactions, in biofilm formation by providing cysteine and via another mechanism not yet understood, in ofloxacin and tellurite resistance as well as in cysteine desulfurization. Some of these activities involve binding of CysK to another cellular partner, where the complex is regulated by the availability of OAS and/or sulfide (H2S). The aim of this study is to present an overview of current knowledge of multiple functions performed by CysK and identifying structural features involved in alternate functions. Due to possible role in disease, promoting or inhibiting a "moonlighting" function of CysK could be a target for developing novel therapeutic interventions.
Collapse
|
14
|
Magalhães J, Franko N, Annunziato G, Pieroni M, Benoni R, Nikitjuka A, Mozzarelli A, Bettati S, Karawajczyk A, Jirgensons A, Campanini B, Costantino G. Refining the structure-activity relationships of 2-phenylcyclopropane carboxylic acids as inhibitors of O-acetylserine sulfhydrylase isoforms. J Enzyme Inhib Med Chem 2018; 34:31-43. [PMID: 30362368 PMCID: PMC6217552 DOI: 10.1080/14756366.2018.1518959] [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] [Indexed: 12/17/2022] Open
Abstract
The lack of efficacy of current antibacterials to treat multidrug resistant bacteria poses a life-threatening alarm. In order to develop enhancers of the antibacterial activity, we carried out a medicinal chemistry campaign aiming to develop inhibitors of enzymes that synthesise cysteine and belong to the reductive sulphur assimilation pathway, absent in mammals. Previous studies have provided a novel series of inhibitors for O-acetylsulfhydrylase – a key enzyme involved in cysteine biosynthesis. Despite displaying nanomolar affinity, the most active representative of the series was not able to interfere with bacterial growth, likely due to poor permeability. Therefore, we rationally modified the structure of the hit compound with the aim of promoting their passage through the outer cell membrane porins. The new series was evaluated on the recombinant enzyme from Salmonella enterica serovar Typhimurium, with several compounds able to keep nanomolar binding affinity despite the extent of chemical manipulation.
Collapse
Affiliation(s)
- Joana Magalhães
- a P4T group, Department of Food and Drug, University of Parma, Parma, Italy
| | - Nina Franko
- b Laboratory of Biochemistry and Molecular Biology, Department of Food and Drug , University of Parma , Parma , Italy
| | | | - Marco Pieroni
- a P4T group, Department of Food and Drug, University of Parma, Parma, Italy
| | - Roberto Benoni
- b Laboratory of Biochemistry and Molecular Biology, Department of Food and Drug , University of Parma , Parma , Italy
| | - Anna Nikitjuka
- c Latvian Institute of Organic Synthesis , Riga , Latvia
| | - Andrea Mozzarelli
- b Laboratory of Biochemistry and Molecular Biology, Department of Food and Drug , University of Parma , Parma , Italy.,d National Institute of Biostructures and Biosystems , Rome , Italy.,e Institute of Biophysics , Pisa , Italy
| | - Stefano Bettati
- b Laboratory of Biochemistry and Molecular Biology, Department of Food and Drug , University of Parma , Parma , Italy.,f Department of Neurosciences , University of Parma , Parma , Italy
| | | | | | - Barbara Campanini
- b Laboratory of Biochemistry and Molecular Biology, Department of Food and Drug , University of Parma , Parma , Italy
| | - Gabriele Costantino
- a P4T group, Department of Food and Drug, University of Parma, Parma, Italy.,h Centro Interdipartimentale Misure (CIM)'G. Casnati', University of Parma , Parma , Italy
| |
Collapse
|
15
|
Franko N, Grammatoglou K, Campanini B, Costantino G, Jirgensons A, Mozzarelli A. Inhibition of O-acetylserine sulfhydrylase by fluoroalanine derivatives. J Enzyme Inhib Med Chem 2018; 33:1343-1351. [PMID: 30251899 PMCID: PMC6161599 DOI: 10.1080/14756366.2018.1504040] [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] [Indexed: 01/22/2023] Open
Abstract
O-acetylserine sulfhydrylase (OASS) is the pyridoxal 5'-phosphate dependent enzyme that catalyses the formation of L-cysteine in bacteria and plants. Its inactivation is pursued as a strategy for the identification of novel antibiotics that, targeting dispensable proteins, holds a great promise for circumventing resistance development. In the present study, we have investigated the reactivity of Salmonella enterica serovar Typhimurium OASS-A and OASS-B isozymes with fluoroalanine derivatives. Monofluoroalanine reacts with OASS-A and OASS-B forming either a stable or a metastable α-aminoacrylate Schiff's base, respectively, as proved by spectral changes. This finding indicates that monofluoroalanine is a substrate analogue, as previously found for other beta-halogenalanine derivatives. Trifluoroalanine caused different and time-dependent absorbance and fluorescence spectral changes for the two isozymes and is associated with irreversible inhibition. The time course of enzyme inactivation was found to be characterised by a biphasic behaviour. Partially distinct inactivation mechanisms for OASS-A and OASS-B are proposed.
Collapse
Affiliation(s)
- Nina Franko
- a Food and Drug Department , University of Parma , Parma , Italy
| | | | | | | | | | - Andrea Mozzarelli
- a Food and Drug Department , University of Parma , Parma , Italy.,c National Research Council , Institute of Biophysics , Pisa , Italy
| |
Collapse
|
16
|
Magalhães J, Franko N, Annunziato G, Welch M, Dolan SK, Bruno A, Mozzarelli A, Armao S, Jirgensons A, Pieroni M, Costantino G, Campanini B. Discovery of novel fragments inhibiting O-acetylserine sulphhydrylase by combining scaffold hopping and ligand-based drug design. J Enzyme Inhib Med Chem 2018; 33:1444-1452. [PMID: 30221554 PMCID: PMC6147075 DOI: 10.1080/14756366.2018.1512596] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Several bacteria rely on the reductive sulphur assimilation pathway, absent in mammals, to synthesise cysteine. Reduction of virulence and decrease in antibiotic resistance have already been associated with mutations on the genes that codify cysteine biosynthetic enzymes. Therefore, inhibition of cysteine biosynthesis has emerged as a promising strategy to find new potential agents for the treatment of bacterial infection. Following our previous efforts to explore OASS inhibition and to expand and diversify our library, a scaffold hopping approach was carried out, with the aim of identifying a novel fragment for further development. This novel chemical tool, endowed with favourable pharmacological characteristics, was successfully developed, and a preliminary Structure–Activity Relationship investigation was carried out.
Collapse
Affiliation(s)
- Joana Magalhães
- a P4T group, Department of Food and Drug , University of Parma , Parma , Italy
| | - Nina Franko
- b Laboratory of Biochemistry and Molecular Biology, Department of Food and Drug , University of Parma , Parma , Italy
| | | | - Martin Welch
- c Department of Biochemistry , Cambridge University , Cambridge , United Kingdom
| | - Stephen K Dolan
- c Department of Biochemistry , Cambridge University , Cambridge , United Kingdom
| | - Agostino Bruno
- d Experimental Therapeutics Program , IFOM - The FIRC Institute for Molecular Oncology Foundation , Milano , Italy
| | - Andrea Mozzarelli
- b Laboratory of Biochemistry and Molecular Biology, Department of Food and Drug , University of Parma , Parma , Italy.,e National Institute of Biostructures and Biosystems , Rome , Italy.,f Institute of Biophysics, CNR , Pisa , Italy
| | - Stefano Armao
- g Centro Interdipartimentale "Biopharmanet-tec", Università degli Studi di Parma , Parma , Italy
| | | | - Marco Pieroni
- a P4T group, Department of Food and Drug , University of Parma , Parma , Italy
| | - Gabriele Costantino
- a P4T group, Department of Food and Drug , University of Parma , Parma , Italy.,i Centro Interdipartimentale Misure (CIM)'G. Casnati', University of Parma , Parma , Italy
| | - Barbara Campanini
- b Laboratory of Biochemistry and Molecular Biology, Department of Food and Drug , University of Parma , Parma , Italy
| |
Collapse
|
17
|
Magalhães J, Annunziato G, Franko N, Pieroni M, Campanini B, Bruno A, Costantino G. Integration of Enhanced Sampling Methods with Saturation Transfer Difference Experiments to Identify Protein Druggable Pockets. J Chem Inf Model 2018; 58:710-723. [DOI: 10.1021/acs.jcim.7b00733] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Joana Magalhães
- Food and Drug Department, P4T group, Parco Area Delle Scienze 27/A−43124, Parma, Italy
| | | | - Nina Franko
- Food and Drug Department, Laboratory of Biochemistry and Molecular Biology, Parco Area Delle Scienze 23/A−43124, Parma, Italy
| | - Marco Pieroni
- Food and Drug Department, P4T group, Parco Area Delle Scienze 27/A−43124, Parma, Italy
| | - Barbara Campanini
- Food and Drug Department, Laboratory of Biochemistry and Molecular Biology, Parco Area Delle Scienze 23/A−43124, Parma, Italy
| | - Agostino Bruno
- Food and Drug Department, P4T group, Parco Area Delle Scienze 27/A−43124, Parma, Italy
- Experimental Therapeutics Program, IFOM−The FIRC Institute for Molecular Oncology Foundation, Via Adamello 16−20139, Milano, Italy
| | - Gabriele Costantino
- Food and Drug Department, P4T group, Parco Area Delle Scienze 27/A−43124, Parma, Italy
| |
Collapse
|
18
|
Benoni R, Beck CM, Garza-Sánchez F, Bettati S, Mozzarelli A, Hayes CS, Campanini B. Activation of an anti-bacterial toxin by the biosynthetic enzyme CysK: mechanism of binding, interaction specificity and competition with cysteine synthase. Sci Rep 2017; 7:8817. [PMID: 28821763 PMCID: PMC5562914 DOI: 10.1038/s41598-017-09022-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 07/20/2017] [Indexed: 12/20/2022] Open
Abstract
Contact-dependent growth inhibition (CDI) is a wide-spread mechanism of inter-bacterial competition. CDI+ bacteria deliver CdiA-CT toxins into neighboring bacteria and produce specific immunity proteins that protect against self-intoxication. The CdiA-CT toxin from uropathogenic Escherichia coli 536 is a latent tRNase that is only active when bound to the cysteine biosynthetic enzyme CysK. Remarkably, the CysK:CdiA-CT binding interaction mimics the ‘cysteine synthase’ complex of CysK:CysE. The C-terminal tails of CysE and CdiA-CT each insert into the CysK active-site cleft to anchor the respective complexes. The dissociation constant for CysK:CdiA-CT (Kd ~ 11 nM) is comparable to that of the E. coli cysteine synthase complex (Kd ~ 6 nM), and both complexes bind through a two-step mechanism with a slow isomerization phase after the initial encounter. However, the second-order rate constant for CysK:CdiA-CT binding is two orders of magnitude slower than that of the cysteine synthase complex, suggesting that CysE should outcompete the toxin for CysK occupancy. However, we find that CdiA-CT can effectively displace CysE from pre-formed cysteine synthase complexes, enabling toxin activation even in the presence of excess competing CysE. This adventitious binding, coupled with the very slow rate of CysK:CdiA-CT dissociation, ensures robust nuclease activity in target bacteria.
Collapse
Affiliation(s)
- Roberto Benoni
- Dipartimento di Medicina e Chirurgia, Università di Parma, Parma, Italy.,Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Praha, Czech Republic
| | - Christina M Beck
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA.,Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Fernando Garza-Sánchez
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Stefano Bettati
- Dipartimento di Medicina e Chirurgia, Università di Parma, Parma, Italy.,Istituto Nazionale Biostrutture e Biosistemi, Rome, Italy
| | - Andrea Mozzarelli
- Istituto Nazionale Biostrutture e Biosistemi, Rome, Italy.,Dipartimento di Scienze degli Alimenti e del Farmaco, Università di Parma, Parma, Italy
| | - Christopher S Hayes
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA. .,Biomolecular Science and Engineering Program, University of California, Santa Barbara, Santa Barbara, CA, USA.
| | - Barbara Campanini
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università di Parma, Parma, Italy.
| |
Collapse
|
19
|
Annunziato G, Pieroni M, Benoni R, Campanini B, Pertinhez TA, Pecchini C, Bruno A, Magalhães J, Bettati S, Franko N, Mozzarelli A, Costantino G. Cyclopropane-1,2-dicarboxylic acids as new tools for the biophysical investigation of O-acetylserine sulfhydrylases by fluorimetric methods and saturation transfer difference (STD) NMR. J Enzyme Inhib Med Chem 2016; 31:78-87. [DOI: 10.1080/14756366.2016.1218486] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Affiliation(s)
| | | | - Roberto Benoni
- Department of Neurosciences, University of Parma, Parma, Italy,
| | | | - Thelma A. Pertinhez
- Department of Biochemical, Biotechnological and Translational Sciences, University of Parma, Parma, Italy,
- Transfusion Medicine Unit, ASMN-IRCCS, Reggio, Emilia, Italy,
| | | | | | | | - Stefano Bettati
- National Institute of Biostructures and Biosystems, Rome, Italy, and
| | | | - Andrea Mozzarelli
- Department of Pharmacy, and
- National Institute of Biostructures and Biosystems, Rome, Italy, and
- Institute of Biophysics, CNR, Pisa, Italy
| | | |
Collapse
|
20
|
Brunner K, Maric S, Reshma RS, Almqvist H, Seashore-Ludlow B, Gustavsson AL, Poyraz Ö, Yogeeswari P, Lundbäck T, Vallin M, Sriram D, Schnell R, Schneider G. Inhibitors of the Cysteine Synthase CysM with Antibacterial Potency against Dormant Mycobacterium tuberculosis. J Med Chem 2016; 59:6848-59. [DOI: 10.1021/acs.jmedchem.6b00674] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Katharina Brunner
- Division of Molecular Structural Biology, Department of Medical Biochemistry & Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden
| | - Selma Maric
- Division of Molecular Structural Biology, Department of Medical Biochemistry & Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden
| | - Rudraraju Srilakshmi Reshma
- Drug Discovery Research Laboratory, Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Shameerpet, R.R. District, Hyderabad 500078, Andhra Pradesh India
| | - Helena Almqvist
- Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine & Chemical Biology, Department of Medical Biochemistry & Biophysics, Karolinska Institutet, S-171 65 Solna, Sweden
| | - Brinton Seashore-Ludlow
- Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine & Chemical Biology, Department of Medical Biochemistry & Biophysics, Karolinska Institutet, S-171 65 Solna, Sweden
| | - Anna-Lena Gustavsson
- Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine & Chemical Biology, Department of Medical Biochemistry & Biophysics, Karolinska Institutet, S-171 65 Solna, Sweden
| | - Ömer Poyraz
- Division of Molecular Structural Biology, Department of Medical Biochemistry & Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden
| | - Perumal Yogeeswari
- Drug Discovery Research Laboratory, Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Shameerpet, R.R. District, Hyderabad 500078, Andhra Pradesh India
| | - Thomas Lundbäck
- Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine & Chemical Biology, Department of Medical Biochemistry & Biophysics, Karolinska Institutet, S-171 65 Solna, Sweden
| | - Michaela Vallin
- Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine & Chemical Biology, Department of Medical Biochemistry & Biophysics, Karolinska Institutet, S-171 65 Solna, Sweden
| | - Dharmarajan Sriram
- Drug Discovery Research Laboratory, Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Shameerpet, R.R. District, Hyderabad 500078, Andhra Pradesh India
| | - Robert Schnell
- Division of Molecular Structural Biology, Department of Medical Biochemistry & Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden
| | - Gunter Schneider
- Division of Molecular Structural Biology, Department of Medical Biochemistry & Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden
| |
Collapse
|
21
|
Annunziato G, Angeli A, D'Alba F, Bruno A, Pieroni M, Vullo D, De Luca V, Capasso C, Supuran CT, Costantino G. Discovery of New Potential Anti-Infective Compounds Based on Carbonic Anhydrase Inhibitors by Rational Target-Focused Repurposing Approaches. ChemMedChem 2016; 11:1904-14. [PMID: 27304878 DOI: 10.1002/cmdc.201600180] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 05/16/2016] [Indexed: 12/31/2022]
Abstract
In academia, compound recycling represents an alternative drug discovery strategy to identify new pharmaceutical targets from a library of chemical compounds available in house. Herein we report the application of a rational target-based drug-repurposing approach to find diverse applications for our in-house collection of compounds. The carbonic anhydrase (CA, EC 4.2.1.1) metalloenzyme superfamily was identified as a potential target of our compounds. The combination of a thoroughly validated docking screening protocol, together with in vitro assays against various CA families and isoforms, allowed us to identify two unprecedented chemotypes as CA inhibitors. The identified compounds have the capacity to preferentially bind pathogenic (bacterial/protozoan) CAs over human isoforms and represent excellent hits for further optimization in hit-to-lead campaigns.
Collapse
Affiliation(s)
- Giannamaria Annunziato
- Università degli Studi di Parma, Dipartimento di Farmacia, P4T group, Parco Area delle Scienze, Via G.P. Usberti 27A, 43121, Parma, Italy
| | - Andrea Angeli
- Università degli Studi di Firenze, Neurofarba Dept., Section of Pharmaceutical and Nutriceutical Sciences, Via U. Schiff 6, 50019, Sesto Fiorentino, Florence, Italy
| | - Francesca D'Alba
- Università degli Studi di Parma, Dipartimento di Farmacia, P4T group, Parco Area delle Scienze, Via G.P. Usberti 27A, 43121, Parma, Italy
| | - Agostino Bruno
- Università degli Studi di Parma, Dipartimento di Farmacia, P4T group, Parco Area delle Scienze, Via G.P. Usberti 27A, 43121, Parma, Italy.
| | - Marco Pieroni
- Università degli Studi di Parma, Dipartimento di Farmacia, P4T group, Parco Area delle Scienze, Via G.P. Usberti 27A, 43121, Parma, Italy
| | - Daniela Vullo
- Università degli Studi di Firenze, Polo Scientifico, Laboratorio di Chimica Bioinorganica, Rm. 188, Via della Lastruccia 3, 50019, Sesto Fiorentino, Florence, Italy
| | - Viviana De Luca
- Istituto di Bioscienze e Biorisorse, CNR, Via Pietro Castellino 111, 80131, Napoli, Italy
| | - Clemente Capasso
- Istituto di Bioscienze e Biorisorse, CNR, Via Pietro Castellino 111, 80131, Napoli, Italy
| | - Claudiu T Supuran
- Università degli Studi di Firenze, Neurofarba Dept., Section of Pharmaceutical and Nutriceutical Sciences, Via U. Schiff 6, 50019, Sesto Fiorentino, Florence, Italy. .,Università degli Studi di Firenze, Polo Scientifico, Laboratorio di Chimica Bioinorganica, Rm. 188, Via della Lastruccia 3, 50019, Sesto Fiorentino, Florence, Italy.
| | - Gabriele Costantino
- Università degli Studi di Parma, Dipartimento di Farmacia, P4T group, Parco Area delle Scienze, Via G.P. Usberti 27A, 43121, Parma, Italy
| |
Collapse
|
22
|
Benoni R, Pertinhez TA, Spyrakis F, Davalli S, Pellegrino S, Paredi G, Pezzotti A, Bettati S, Campanini B, Mozzarelli A. Structural insight into the interaction ofO-acetylserine sulfhydrylase with competitive, peptidic inhibitors by saturation transfer difference-NMR. FEBS Lett 2016; 590:943-53. [DOI: 10.1002/1873-3468.12126] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 02/26/2016] [Accepted: 03/01/2016] [Indexed: 11/10/2022]
Affiliation(s)
| | - Thelma A. Pertinhez
- Department of Oncology and Advanced Techniques; Arcispedale Santa Maria Nuova-IRCCS; Reggio Emilia Italy
| | | | | | - Sara Pellegrino
- Department of Pharmaceutical Sciences; Section of General and Organic Chemistry ‘A. Marchesini’; University of Milan; Italy
| | | | | | - Stefano Bettati
- Department of Neurosciences; University of Parma; Italy
- National Institute for Biostructures and Biosystems; Rome Italy
| | | | - Andrea Mozzarelli
- Department of Pharmacy; University of Parma; Italy
- National Institute for Biostructures and Biosystems; Rome Italy
- Institute of Biophysics; CNR; Pisa Italy
| |
Collapse
|
23
|
Pieroni M, Annunziato G, Beato C, Wouters R, Benoni R, Campanini B, Pertinhez TA, Bettati S, Mozzarelli A, Costantino G. Rational Design, Synthesis, and Preliminary Structure–Activity Relationships of α-Substituted-2-Phenylcyclopropane Carboxylic Acids as Inhibitors of Salmonella typhimurium O-Acetylserine Sulfhydrylase. J Med Chem 2016; 59:2567-78. [DOI: 10.1021/acs.jmedchem.5b01775] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
| | | | | | | | | | | | | | - Stefano Bettati
- Department
of Neurosciences, University of Parma, Via Volturno, 39, 43125 Parma, Italy
- National Institute of Biostructures and Biosystems, Viale delle Medaglie d’Oro 305, 00136 Rome, Italy
| | - Andrea Mozzarelli
- National Institute of Biostructures and Biosystems, Viale delle Medaglie d’Oro 305, 00136 Rome, Italy
- Institute of Biophysics, CNR, /o
Area di Ricerca San Cataldo, Via G. Moruzzi N° 1, 56124 Pisa, Italy
| | | |
Collapse
|
24
|
Stockton KP, Greatrex BW. Synthesis of enantiopure cyclopropyl esters from (−)-levoglucosenone. Org Biomol Chem 2016; 14:7520-8. [DOI: 10.1039/c6ob00933f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Levoglucosenone was converted into the GABAC agonists (−)-TAMP, (+)-TAMP and an advanced intermediate used for the synthesis of the selective glutamate receptor antagonist PCCG-4.
Collapse
Affiliation(s)
- Kieran P. Stockton
- School of Science and Technology
- University of New England
- Armidale
- Australia
| | - Ben W. Greatrex
- School of Science and Technology
- University of New England
- Armidale
- Australia
| |
Collapse
|
25
|
Mori M, Jeelani G, Masuda Y, Sakai K, Tsukui K, Waluyo D, Tarwadi, Watanabe Y, Nonaka K, Matsumoto A, Ōmura S, Nozaki T, Shiomi K. Identification of natural inhibitors of Entamoeba histolytica cysteine synthase from microbial secondary metabolites. Front Microbiol 2015; 6:962. [PMID: 26441896 PMCID: PMC4568418 DOI: 10.3389/fmicb.2015.00962] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 08/31/2015] [Indexed: 11/13/2022] Open
Abstract
Amebiasis is a common worldwide diarrheal disease, caused by the protozoan parasite, Entamoeba histolytica. Metronidazole has been a drug of choice against amebiasis for decades despite its known side effects and low efficacy against asymptomatic cyst carriers. E. histolytica is also capable of surviving sub-therapeutic levels of metronidazole in vitro. Novel drugs with different mode of action are therefore urgently needed. The sulfur assimilatory de novo L-cysteine biosynthetic pathway is essential for various cellular activities, including the proliferation and anti-oxidative defense of E. histolytica. Since the pathway, consisting of two reactions catalyzed by serine acetyltransferase (SAT) and cysteine synthase (CS, O-acetylserine sulfhydrylase), does not exist in humans, it is a rational drug target against amebiasis. To discover inhibitors against the CS of E. histolytica (EhCS), the compounds of Kitasato Natural Products Library were screened against two recombinant CS isozymes: EhCS1 and EhCS3. Nine compounds inhibited EhCS1 and EhCS3 with IC50 values of 0.31-490 μM. Of those, seven compounds share a naphthoquinone moiety, indicating the structural importance of the moiety for binding to the active site of EhCS1 and EhCS3. We further screened >9,000 microbial broths for CS inhibition and purified two compounds, xanthofulvin and exophillic acid from fungal broths. Xanthofulvin inhibited EhCS1 and EhCS3. Exophillic acid showed high selectivity against EhCS1, but exhibited no inhibition against EhCS3. In vitro anti-amebic activity of the 11 EhCS inhibitors was also examined. Deacetylkinamycin C and nanaomycin A showed more potent amebicidal activity with IC50 values of 18 and 0.8 μM, respectively, in the cysteine deprived conditions. The differential sensitivity of trophozoites against deacetylkinamycin C in the presence or absence of L-cysteine in the medium and the IC50 values against EhCS suggest the amebicidal effect of deacetylkinamycin C is due to CS inhibition.
Collapse
Affiliation(s)
- Mihoko Mori
- Kitasato Institute for Life Sciences, Kitasato UniversityTokyo, Japan
- Graduate School of Infection Control Sciences, Kitasato UniversityTokyo, Japan
| | - Ghulam Jeelani
- Department of Parasitology, National Institute of Infectious DiseasesTokyo, Japan
| | - Yui Masuda
- Graduate School of Infection Control Sciences, Kitasato UniversityTokyo, Japan
| | - Kazunari Sakai
- Graduate School of Infection Control Sciences, Kitasato UniversityTokyo, Japan
| | - Kumiko Tsukui
- Department of Parasitology, National Institute of Infectious DiseasesTokyo, Japan
| | - Danang Waluyo
- Biotech Center, Badan Pengkajian Dan Penerapan TeknologiBanten, Indonesia
| | - Tarwadi
- Biotech Center, Badan Pengkajian Dan Penerapan TeknologiBanten, Indonesia
| | - Yoshio Watanabe
- Research and Development Division, MicroBiopharm Japan Co. LtdIwata, Japan
| | - Kenichi Nonaka
- Kitasato Institute for Life Sciences, Kitasato UniversityTokyo, Japan
- Graduate School of Infection Control Sciences, Kitasato UniversityTokyo, Japan
| | - Atsuko Matsumoto
- Kitasato Institute for Life Sciences, Kitasato UniversityTokyo, Japan
- Graduate School of Infection Control Sciences, Kitasato UniversityTokyo, Japan
| | - Satoshi Ōmura
- Kitasato Institute for Life Sciences, Kitasato UniversityTokyo, Japan
| | - Tomoyoshi Nozaki
- Department of Parasitology, National Institute of Infectious DiseasesTokyo, Japan
- Graduate School of Life and Environmental Sciences, University of TsukubaTsukuba, Japan
| | - Kazuro Shiomi
- Kitasato Institute for Life Sciences, Kitasato UniversityTokyo, Japan
- Graduate School of Infection Control Sciences, Kitasato UniversityTokyo, Japan
| |
Collapse
|
26
|
Beato C, Pecchini C, Cocconcelli C, Campanini B, Marchetti M, Pieroni M, Mozzarelli A, Costantino G. Cyclopropane derivatives as potential human serine racemase inhibitors: unveiling novel insights into a difficult target. J Enzyme Inhib Med Chem 2015; 31:645-52. [PMID: 26133542 DOI: 10.3109/14756366.2015.1057720] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
d-Serine is the co-agonist of NMDA receptors and binds to the so-called glycine site. d-Serine is synthesized by human serine racemase (SR). Over activation of NMDA receptors is involved in many neurodegenerative diseases and, therefore, the inhibition of SR might represent a novel strategy for the treatment of these pathologies. SR is a very difficult target, with only few compounds so far identified exhibiting weak inhibitory activity. This study was aimed at the identification of novel SR inhibitor by mimicking malonic acid, the best-known SR inhibitor, with a cyclopropane scaffold. We developed, synthesized, and tested a series of cyclopropane dicarboxylic acid derivatives, complementing the synthetic effort with molecular docking. We identified few compounds that bind SR in high micromolar range with a lack of significant correlation between experimental and predicted binding affinities. The thorough analysis of the results can be exploited for the development of more potent SR inhibitors.
Collapse
Affiliation(s)
- Claudia Beato
- a Dipartimento di Farmacia , Università degli studi di Parma , Parma , Italy
| | - Chiara Pecchini
- a Dipartimento di Farmacia , Università degli studi di Parma , Parma , Italy
| | - Chiara Cocconcelli
- a Dipartimento di Farmacia , Università degli studi di Parma , Parma , Italy
| | - Barbara Campanini
- a Dipartimento di Farmacia , Università degli studi di Parma , Parma , Italy
| | | | - Marco Pieroni
- a Dipartimento di Farmacia , Università degli studi di Parma , Parma , Italy
| | - Andrea Mozzarelli
- a Dipartimento di Farmacia , Università degli studi di Parma , Parma , Italy .,b Istituto Nazionale Biostrutture e Biosistemi -- Consorzio Interuniversitario , Roma , Italy , and.,c Istituto di Biofisica, CNR , Pisa , Italy
| | - Gabriele Costantino
- a Dipartimento di Farmacia , Università degli studi di Parma , Parma , Italy
| |
Collapse
|
27
|
Schnell R, Sriram D, Schneider G. Pyridoxal-phosphate dependent mycobacterial cysteine synthases: Structure, mechanism and potential as drug targets. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1854:1175-83. [PMID: 25484279 DOI: 10.1016/j.bbapap.2014.11.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 11/26/2014] [Accepted: 11/27/2014] [Indexed: 01/23/2023]
Abstract
The alarming increase of drug resistance in Mycobacterium tuberculosis strains poses a severe threat to human health. Chemotherapy is particularly challenging because M. tuberculosis can persist in the lungs of infected individuals; estimates of the WHO indicate that about 1/3 of the world population is infected with latent tuberculosis providing a large reservoir for relapse and subsequent spread of the disease. Persistent M. tuberculosis shows considerable tolerance towards conventional antibiotics making treatment particularly difficult. In this phase the bacilli are exposed to oxygen and nitrogen radicals generated as part of the host response and redox-defense mechanisms are thus vital for the survival of the pathogen. Sulfur metabolism and de novo cysteine biosynthesis have been shown to be important for the redox homeostasis in persistent M. tuberculosis and these pathways could provide promising targets for novel antibiotics for the treatment of the latent form of the disease. Recent research has provided evidence for three de novo metabolic routes of cysteine biosynthesis in M. tuberculosis, each with a specific PLP dependent cysteine synthase with distinct substrate specificities. In this review we summarize our present understanding of these pathways, with a focus on the advances on functional and mechanistic characterization of mycobacterial PLP dependent cysteine synthases, their role in the various pathways to cysteine, and first attempts to develop specific inhibitors of mycobacterial cysteine biosynthesis. This article is part of a Special Issue entitled: Cofactor-dependent proteins: evolution, chemical diversity and bio-applications.
Collapse
Affiliation(s)
- Robert Schnell
- Department of Medical Biochemistry & Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden
| | - Dharmarajan Sriram
- Drug Discovery Research Laboratory, Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Shameerpet, R.R. District, Hyderabad-500078, Andhra Pradesh, India
| | - Gunter Schneider
- Department of Medical Biochemistry & Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden.
| |
Collapse
|
28
|
Marchetti M, Bruno S, Campanini B, Bettati S, Peracchi A, Mozzarelli A. Regulation of human serine racemase activity and dynamics by halides, ATP and malonate. Amino Acids 2014; 47:163-73. [PMID: 25331425 DOI: 10.1007/s00726-014-1856-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 10/09/2014] [Indexed: 02/03/2023]
Abstract
D-Serine is a non-proteinogenic amino acid that acts as a co-agonist of the NMDA receptors in the central nervous system. D-Serine is produced by human serine racemase (hSR), a homodimeric pyridoxal 5'-phosphate (PLP)-dependent enzyme that also catalyzes the physiologically relevant β-elimination of both L- and D-serine to pyruvate and ammonia. After improving the protein purification yield and stability, which had so far limited the biochemical characterization of hSR, we found that the catalytic activity is affected by halides, in the order fluoride > chloride > bromide. On the contrary, iodide elicited a complete inhibition, accompanied by a modulation of the tautomeric equilibrium of the internal aldimine. We also investigated the reciprocal effects of ATP and malonate, an inhibitor that reversibly binds at the active site, 20 Å away from the ATP-binding site. ATP increased ninefold the affinity of hSR for malonate and malonate increased 100-fold that of ATP, confirming an allosteric interaction between the two binding sites. To further investigate this allosteric communication, we probed the active site accessibility by quenching of the coenzyme fluorescence in the absence and presence of ATP. We found that ATP stabilizes a closed conformation of the external aldimine Schiff base, suggesting a possible mechanism for ATP-induced hSR activation.
Collapse
|
29
|
Spyrakis F, Cellini B, Bruno S, Benedetti P, Carosati E, Cruciani G, Micheli F, Felici A, Cozzini P, Kellogg GE, Voltattorni CB, Mozzarelli A. Targeting cystalysin, a virulence factor of treponema denticola-supported periodontitis. ChemMedChem 2014; 9:1501-11. [PMID: 24616267 DOI: 10.1002/cmdc.201300527] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 02/13/2014] [Indexed: 01/01/2023]
Abstract
Cystalysin from Treponema denticola is a pyridoxal 5'-phosphate dependent lyase that catalyzes the formation of pyruvate, ammonia, and sulfide from cysteine. It is a virulence factor in adult periodontitis because its reaction contributes to hemolysis, which sustains the pathogen. Therefore, it was proposed as a potential antimicrobial target. To identify specific inhibitors by structure-based in silico methods, we first validated the crystal structure of cystalysin as a reliable starting point for the design of ligands. By using single-crystal absorption microspectrophotometry, we found that the enzyme in the crystalline state, with respect to that in solution, exhibits: 1) the same absorption spectra for the catalytic intermediates, 2) a close pKa value for the residue controlling the keto enamine ionization, and 3) similar reactivity with glycine, L-serine, L-methionine, and the nonspecific irreversible inhibitor aminoethoxyvinylglycine. Next, we screened in silico a library of 9357 compounds with the Fingerprints for Ligands and Proteins (FLAP) software, by using the three-dimensional structure of cystalysin as a template. From the library, 17 compounds were selected and experimentally evaluated by enzyme assays and spectroscopic methods. Two compounds were found to competitively inhibit recombinant T. denticola cystalysin, with inhibition constant (Ki ) values of 25 and 37 μM. One of them exhibited a minimum inhibitory concentration (MIC) value of 64 μg mL(-1) on Moraxella catarrhalis ATCC 23246, which proves its ability to cross bacterial membranes.
Collapse
Affiliation(s)
- Francesca Spyrakis
- Department of Food Sciences, University of Parma, Parma (Italy); Current address: Department of Life Sciences, University of Modena and Reggio Emilia, Modena (Italy)
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Spyrakis F, Singh R, Cozzini P, Campanini B, Salsi E, Felici P, Raboni S, Benedetti P, Cruciani G, Kellogg GE, Cook PF, Mozzarelli A. Isozyme-specific ligands for O-acetylserine sulfhydrylase, a novel antibiotic target. PLoS One 2013; 8:e77558. [PMID: 24167577 PMCID: PMC3805590 DOI: 10.1371/journal.pone.0077558] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 09/03/2013] [Indexed: 01/06/2023] Open
Abstract
The last step of cysteine biosynthesis in bacteria and plants is catalyzed by O-acetylserine sulfhydrylase. In bacteria, two isozymes, O-acetylserine sulfhydrylase-A and O-acetylserine sulfhydrylase-B, have been identified that share similar binding sites, although the respective specific functions are still debated. O-acetylserine sulfhydrylase plays a key role in the adaptation of bacteria to the host environment, in the defense mechanisms to oxidative stress and in antibiotic resistance. Because mammals synthesize cysteine from methionine and lack O-acetylserine sulfhydrylase, the enzyme is a potential target for antimicrobials. With this aim, we first identified potential inhibitors of the two isozymes via a ligand- and structure-based in silico screening of a subset of the ZINC library using FLAP. The binding affinities of the most promising candidates were measured in vitro on purified O-acetylserine sulfhydrylase-A and O-acetylserine sulfhydrylase-B from Salmonella typhimurium by a direct method that exploits the change in the cofactor fluorescence. Two molecules were identified with dissociation constants of 3.7 and 33 µM for O-acetylserine sulfhydrylase-A and O-acetylserine sulfhydrylase-B, respectively. Because GRID analysis of the two isoenzymes indicates the presence of a few common pharmacophoric features, cross binding titrations were carried out. It was found that the best binder for O-acetylserine sulfhydrylase-B exhibits a dissociation constant of 29 µM for O-acetylserine sulfhydrylase-A, thus displaying a limited selectivity, whereas the best binder for O-acetylserine sulfhydrylase-A exhibits a dissociation constant of 50 µM for O-acetylserine sulfhydrylase-B and is thus 8-fold selective towards the former isozyme. Therefore, isoform-specific and isoform-independent ligands allow to either selectively target the isozyme that predominantly supports bacteria during infection and long-term survival or to completely block bacterial cysteine biosynthesis.
Collapse
Affiliation(s)
| | - Ratna Singh
- Department of Pharmacy, University of Parma, Parma, Italy
| | - Pietro Cozzini
- Department of Food Sciences, University of Parma, Parma, Italy
- National Institute of Biostructures and Biosystems, Rome, Italy
| | - Barbara Campanini
- Department of Pharmacy, University of Parma, Parma, Italy
- * E-mail: (BC); (AM)
| | - Enea Salsi
- Department of Pharmacy, University of Parma, Parma, Italy
| | - Paolo Felici
- Department of Pharmacy, University of Parma, Parma, Italy
| | - Samanta Raboni
- Department of Pharmacy, University of Parma, Parma, Italy
| | | | | | - Glen E. Kellogg
- Department of Medicinal Chemistry and Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Paul F. Cook
- Department of Biochemistry, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Andrea Mozzarelli
- Department of Pharmacy, University of Parma, Parma, Italy
- National Institute of Biostructures and Biosystems, Rome, Italy
- * E-mail: (BC); (AM)
| |
Collapse
|
31
|
Poyraz Ö, Jeankumar VU, Saxena S, Schnell R, Haraldsson M, Yogeeswari P, Sriram D, Schneider G. Structure-Guided Design of Novel Thiazolidine Inhibitors of O-Acetyl Serine Sulfhydrylase from Mycobacterium tuberculosis. J Med Chem 2013; 56:6457-66. [DOI: 10.1021/jm400710k] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Ömer Poyraz
- Division of Molecular Structural Biology, Department of Medical Biochemistry & Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden
| | - Variam Ullas Jeankumar
- Drug Discovery Research Laboratory, Department of Pharmacy, Birla Institute of Technology & Science—Pilani, Hyderabad Campus, Shameerpet, R.R. District, Hyderabad-500078, Andhra Pradesh, India
| | - Shalini Saxena
- Drug Discovery Research Laboratory, Department of Pharmacy, Birla Institute of Technology & Science—Pilani, Hyderabad Campus, Shameerpet, R.R. District, Hyderabad-500078, Andhra Pradesh, India
| | - Robert Schnell
- Division of Molecular Structural Biology, Department of Medical Biochemistry & Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden
| | - Martin Haraldsson
- Division of Molecular Structural Biology, Department of Medical Biochemistry & Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden
| | - Perumal Yogeeswari
- Drug Discovery Research Laboratory, Department of Pharmacy, Birla Institute of Technology & Science—Pilani, Hyderabad Campus, Shameerpet, R.R. District, Hyderabad-500078, Andhra Pradesh, India
| | - Dharmarajan Sriram
- Drug Discovery Research Laboratory, Department of Pharmacy, Birla Institute of Technology & Science—Pilani, Hyderabad Campus, Shameerpet, R.R. District, Hyderabad-500078, Andhra Pradesh, India
| | - Gunter Schneider
- Division of Molecular Structural Biology, Department of Medical Biochemistry & Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden
| |
Collapse
|
32
|
Raj I, Mazumder M, Gourinath S. Molecular basis of ligand recognition by OASS from E. histolytica: insights from structural and molecular dynamics simulation studies. Biochim Biophys Acta Gen Subj 2013; 1830:4573-83. [PMID: 23747298 DOI: 10.1016/j.bbagen.2013.05.041] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 05/08/2013] [Accepted: 05/29/2013] [Indexed: 10/26/2022]
Abstract
BACKGROUND O-acetyl serine sulfhydrylase (OASS) is a pyridoxal phosphate (PLP) dependent enzyme catalyzing the last step of the cysteine biosynthetic pathway. Here we analyze and investigate the factors responsible for recognition and different conformational changes accompanying the binding of various ligands to OASS. METHODS X ray crystallography was used to determine the structures of OASS from Entamoeba histolytica in complex with methionine (substrate analog), isoleucine (inhibitor) and an inhibitory tetra-peptide to 2.00Å, 2.03Å and 1.87Å resolutions, respectively. Molecular dynamics simulations were used to investigate the reasons responsible for the extent of domain movement and cleft closure of the enzyme in presence of different ligands. RESULTS Here we report for the first time an OASS-methionine structure with an unmutated catalytic lysine at the active site. This is also the first OASS structure with a closed active site lacking external aldimine formation. The OASS-isoleucine structure shows the active site cleft in open state. Molecular dynamics studies indicate that cofactor PLP, N88 and G192 form a triad of energy contributors to close the active site upon ligand binding and orientation of the Schiff base forming nitrogen of the ligand is critical for this interaction. CONCLUSIONS Methionine proves to be a better binder to OASS than isoleucine. The β branching of isoleucine does not allow it to reorient itself in suitable conformation near PLP to cause active site closure. GENERAL SIGNIFICANCE Our findings have important implications in designing better inhibitors against OASS across all pathogenic microbial species.
Collapse
Affiliation(s)
- Isha Raj
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | | | | |
Collapse
|
33
|
Bruno A, Amori L, Costantino G. Computational Insights into the Mechanism of Inhibition of OASS-A by a Small Molecule Inhibitor. Mol Inform 2013; 32:447-57. [PMID: 27481665 DOI: 10.1002/minf.201200174] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Accepted: 02/09/2012] [Indexed: 11/09/2022]
Abstract
O-Acetylserine sulfhydrylase (isoform A, OASS-A) is a PLP-dependent enzyme involved in the last step of cysteine biosynthesis in many pathogens. Many microorganisms use cysteine as the main building block for sulfur-containing antioxidants, and cysteine depletion in several pathogens resulted in a reduced antibiotic resistance, thus leading to the identification of OASS as novel suitable molecular targets to overcome antimicrobial resistances. The precise molecular mechanism of OASS-A inhibition by small peptides or by small molecule inhibitors is still unclear. To shed more lights on the structural basis underlying the inhibition mechanism for OASS, we engaged ourselves in studying the dynamic properties of this enzyme. In this paper, we describe a computational study involving unbiased MD simulations of OASS-A from Haemophilus influenzae (HiOASS) in its inhibitor free, PLP-bound form, and in complex with a pentapeptide inhibitor and with UPAR40, a small molecule which we have recently reported as a potent OASS-A inhibitors. We proposed that UPAR40 inhibits HiOASS-A through the stabilization of a closed conformation. Moreover, preliminary docking studies and sequence analysis allow us to speculate about the non-specificity of UPAR40 toward a particular OASS enzyme species or isoforms.
Collapse
Affiliation(s)
- Agostino Bruno
- Department of Pharmacy, Università degli Studi di Parma, Parco Area delle Scienze, Viale G. P. Usberti 27/A, 43124, Parma, Italy
| | - Laura Amori
- Department of Pharmacy, Università degli Studi di Parma, Parco Area delle Scienze, Viale G. P. Usberti 27/A, 43124, Parma, Italy
| | - Gabriele Costantino
- Department of Pharmacy, Università degli Studi di Parma, Parco Area delle Scienze, Viale G. P. Usberti 27/A, 43124, Parma, Italy.
| |
Collapse
|
34
|
Spyrakis F, Felici P, Bayden AS, Salsi E, Miggiano R, Kellogg GE, Cozzini P, Cook PF, Mozzarelli A, Campanini B. Fine tuning of the active site modulates specificity in the interaction of O-acetylserine sulfhydrylase isozymes with serine acetyltransferase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:169-81. [DOI: 10.1016/j.bbapap.2012.09.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 09/10/2012] [Accepted: 09/12/2012] [Indexed: 10/27/2022]
|