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Rice AJ, Pesavento RP, Ren J, Youn I, Kwon Y, Ellepola K, Che CT, Johnson ME, Lee H. Identification of Small Molecule Inhibitors against Staphylococcus aureus Dihydroorotase via HTS. Int J Mol Sci 2021; 22:ijms22189984. [PMID: 34576147 PMCID: PMC8467647 DOI: 10.3390/ijms22189984] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/02/2021] [Accepted: 09/11/2021] [Indexed: 11/16/2022] Open
Abstract
Drug-resistant Staphylococcus aureus is an imminent threat to public health, increasing the importance of drug discovery utilizing unexplored bacterial pathways and enzyme targets. De novo pyrimidine biosynthesis is a specialized, highly conserved pathway implicated in both the survival and virulence of several clinically relevant pathogens. Class I dihydroorotase (DHOase) is a separate and distinct enzyme present in gram positive bacteria (i.e., S. aureus, B. anthracis) that converts carbamoyl-aspartate (Ca-asp) to dihydroorotate (DHO)-an integral step in the de novo pyrimidine biosynthesis pathway. This study sets forth a high-throughput screening (HTS) of 3000 fragment compounds by a colorimetry-based enzymatic assay as a primary screen, identifying small molecule inhibitors of S. aureus DHOase (SaDHOase), followed by hit validation with a direct binding analysis using surface plasmon resonance (SPR). Competition SPR studies of six hit compounds and eight additional analogs with the substrate Ca-asp determined the best compound to be a competitive inhibitor with a KD value of 11 µM, which is 10-fold tighter than Ca-asp. Preliminary structure-activity relationship (SAR) provides the foundation for further structure-based antimicrobial inhibitor design against S. aureus.
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Affiliation(s)
- Amy J. Rice
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA; (A.J.R.); (R.P.P.); (J.R.); (Y.K.)
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA; (I.Y.); (C.-T.C.)
| | - Russell P. Pesavento
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA; (A.J.R.); (R.P.P.); (J.R.); (Y.K.)
- Department of Oral Biology, College of Dentistry, University of Illinois at Chicago, Chicago, IL 60607, USA;
| | - Jinhong Ren
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA; (A.J.R.); (R.P.P.); (J.R.); (Y.K.)
| | - Isoo Youn
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA; (I.Y.); (C.-T.C.)
| | - Youngjin Kwon
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA; (A.J.R.); (R.P.P.); (J.R.); (Y.K.)
- Biophysics Core at the Research Resource Center, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Kassapa Ellepola
- Department of Oral Biology, College of Dentistry, University of Illinois at Chicago, Chicago, IL 60607, USA;
| | - Chun-Tao Che
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA; (I.Y.); (C.-T.C.)
| | - Michael E. Johnson
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA; (A.J.R.); (R.P.P.); (J.R.); (Y.K.)
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA; (I.Y.); (C.-T.C.)
- Correspondence: (M.E.J.); (H.L.); Tel.: +1-312-996-9114 (M.E.J.); +1-312-355-5292 (H.L.)
| | - Hyun Lee
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA; (A.J.R.); (R.P.P.); (J.R.); (Y.K.)
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA; (I.Y.); (C.-T.C.)
- Biophysics Core at the Research Resource Center, University of Illinois at Chicago, Chicago, IL 60607, USA
- Correspondence: (M.E.J.); (H.L.); Tel.: +1-312-996-9114 (M.E.J.); +1-312-355-5292 (H.L.)
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Onyeogaziri FC, Papaneophytou C. A General Guide for the Optimization of Enzyme Assay Conditions Using the Design of Experiments Approach. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2019; 24:587-596. [PMID: 30802413 DOI: 10.1177/2472555219830084] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Many factors must be considered during the optimization of an enzyme assay. These include the choice of buffer and its composition, the type of enzyme and its concentration, as well as the type of substrate and concentrations, the reaction conditions, and the appropriate assay technology. The process of an enzyme assay optimization, in our experience, can take more than 12 weeks using the traditional one-factor-at-a-time approach. In contrast, the design of experiments (DoE) approaches have the potential to speed up the assay optimization process and provide a more detailed evaluation of tested variables. However, not all researchers are aware of DoE approaches or believe that it is easy to employ a DoE approach for the optimization of an assay. In order to facilitate enzyme assay developers to use DoE methodologies, we present in detail the steps required to identify in less than 3 days (1) the factors that significantly affect the activity of an enzyme and (2) the optimal assay conditions using a fractional factorial approach and response surface methodology. This is exemplified with the optimization of assay conditions for the human rhinovirus-3C protease, and the methodology used could be employed as a basic guide for the speedy identification of the optimum assay conditions for any enzyme.
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Affiliation(s)
- Favour Chinyere Onyeogaziri
- 1 Department of Life and Health Sciences, School of Sciences and Engineering, University of Nicosia, Nicosia, Cyprus
| | - Christos Papaneophytou
- 1 Department of Life and Health Sciences, School of Sciences and Engineering, University of Nicosia, Nicosia, Cyprus
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Boulton S, Selvaratnam R, Ahmed R, Van K, Cheng X, Melacini G. Mechanisms of Specific versus Nonspecific Interactions of Aggregation-Prone Inhibitors and Attenuators. J Med Chem 2019; 62:5063-5079. [PMID: 31074269 PMCID: PMC7255057 DOI: 10.1021/acs.jmedchem.9b00258] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A common source of false positives in drug discovery is ligand self-association into large colloidal assemblies that nonspecifically inhibit target proteins. However, the mechanisms of aggregation-based inhibition (ABI) and ABI-attenuation by additives, such as Triton X-100 (TX) and human serum albumin (HSA), are not fully understood. Here, we investigate the molecular basis of ABI and ABI-attenuation through the lens of NMR and coupled thermodynamic cycles. We unexpectedly discover a new class of aggregating ligands that exhibit negligible interactions with proteins but act as competitive sinks for the free inhibitor, resulting in bell-shaped dose-response curves. TX attenuates ABI by converting inhibitory, protein-binding aggregates into nonbinding coaggregates, whereas HSA minimizes nonspecific ligand interactions by functioning as a reservoir for free inhibitor and preventing self-association. Hence, both TX and HSA are useful tools to minimize false positives arising from nonspecific binding but at the cost of potentially introducing false negatives due to suppression of specific interactions.
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Affiliation(s)
- Stephen Boulton
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4L8, Canada
| | - Rajeevan Selvaratnam
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4L8, Canada
- Department of Laboratory Medicine, University Health Network, Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5G 2C4, Canada
| | - Rashik Ahmed
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4L8, Canada
| | - Katherine Van
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4L8, Canada
| | - Xiaodong Cheng
- Department of Integrative Biology and Pharmacology and Texas Therapeutics Institute, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, United States
| | - Giuseppe Melacini
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4L8, Canada
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4L8, Canada
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Ca-asp bound X-ray structure and inhibition of Bacillus anthracis dihydroorotase (DHOase). Bioorg Med Chem 2016; 24:4536-4543. [PMID: 27499369 DOI: 10.1016/j.bmc.2016.07.055] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/22/2016] [Accepted: 07/25/2016] [Indexed: 01/01/2023]
Abstract
Dihydroorotase (DHOase) is the third enzyme in the de novo pyrimidine synthesis pathway and is responsible for the reversible cyclization of carbamyl-aspartate (Ca-asp) to dihydroorotate (DHO). DHOase is further divided into two classes based on several structural characteristics, one of which is the length of the flexible catalytic loop that interacts with the substrate, Ca-asp, regulating the enzyme activity. Here, we present the crystal structure of Class I Bacillus anthracis DHOase with Ca-asp in the active site, which shows the peptide backbone of glycine in the shorter loop forming the necessary hydrogen bonds with the substrate, in place of the two threonines found in Class II DHOases. Despite the differences in the catalytic loop, the structure confirms that the key interactions between the substrate and active site residues are similar between Class I and Class II DHOase enzymes, which we further validated by mutagenesis studies. B. anthracis DHOase is also a potential antibacterial drug target. In order to identify prospective inhibitors, we performed high-throughput screening against several libraries using a colorimetric enzymatic assay and an orthogonal fluorescence thermal binding assay. Surface plasmon resonance was used for determining binding affinity (KD) and competition analysis with Ca-asp. Our results highlight that the primary difference between Class I and Class II DHOase is the catalytic loop. We also identify several compounds that can potentially be further optimized as potential B. anthracis inhibitors.
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Fan RJ, Guan Q, Zhang F, Leng JP, Sun TQ, Guo YL. Benzylic rearrangement stable isotope labeling for quantitation of guanidino and ureido compounds in thyroid tissues by liquid chromatography-electrospray ionization mass spectrometry. Anal Chim Acta 2016; 908:132-40. [PMID: 26826695 DOI: 10.1016/j.aca.2015.12.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 12/18/2015] [Accepted: 12/20/2015] [Indexed: 12/18/2022]
Abstract
Benzylic rearrangement stable isotope labeling (BRSIL) was explored to quantify the guanidino and ureido compounds (GCs and UCs). This method employed a common reagent, benzil, to label the guanidino and ureido groups through nucleophilic attacking then benzylic migrating. The use of BRSIL was investigated in the analysis of five GCs (creatine, l-arginine, homoarginine, 4-guanidinobutyric acid, and methylguanidine) and two UCs (urea and citrulline). The labeling was found simple and specific. The introduction of bi-phenyl group and the generation of nitrogen heterocyclic ring in the benzil-d0/d5 labeled GCs and UCs improved the retention behaviors in liquid chromatography (LC) and increased the sensitivity of electrospray ionization mass spectrometry (ESI MS) detection. The fragment ion pairs of m/z 182/187 and m/z 210/215 from the benzil-d0/d5 tags facilitated the discovery of potential GCs and UCs candidates residing in biological matrices. The use of BRSIL combined with LC-ESI MS was applied for simultaneously quantitation of GCs and UCs in thyroid tissues. It was demonstrated that nine GCs and UCs were detected, six of which were further quantified based on corresponding standards. It was concluded that five GCs and UCs (l-arginine, homoarginine, 4-guanidinobutyric acid, methylguanidine, and citrulline) were statistically significantly different (p < 0.05) between the para-carcinoma and carcinoma thyroid tissue samples.
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Affiliation(s)
- Ruo-Jing Fan
- State Key Laboratory of Organmetallic Chemistry and National Center for Organic Mass Spectrometry in Shanghai, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, People's Republic of China
| | - Qing Guan
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, People's Republic of China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, People's Republic of China
| | - Fang Zhang
- State Key Laboratory of Organmetallic Chemistry and National Center for Organic Mass Spectrometry in Shanghai, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, People's Republic of China.
| | - Jia-Peng Leng
- State Key Laboratory of Organmetallic Chemistry and National Center for Organic Mass Spectrometry in Shanghai, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, People's Republic of China
| | - Tuan-Qi Sun
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, People's Republic of China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, People's Republic of China.
| | - Yin-Long Guo
- State Key Laboratory of Organmetallic Chemistry and National Center for Organic Mass Spectrometry in Shanghai, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, People's Republic of China.
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