1
|
Orr AA, Tao A, Guvench O, MacKerell AD. Site Identification by Ligand Competitive Saturation-Biologics Approach for Structure-Based Protein Charge Prediction. Mol Pharm 2023; 20:2600-2611. [PMID: 37017675 PMCID: PMC10159941 DOI: 10.1021/acs.molpharmaceut.3c00064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]
Abstract
Protein-based therapeutics typically require high concentrations of the active protein, which can lead to protein aggregation and high solution viscosity. Such solution behaviors can limit the stability, bioavailability, and manufacturability of protein-based therapeutics and are directly influenced by the charge of a protein. Protein charge is a system property affected by its environment, including the buffer composition, pH, and temperature. Thus, the charge calculated by summing the charges of each residue in a protein, as is commonly done in computational methods, may significantly differ from the effective charge of the protein as these calculations do not account for contributions from bound ions. Here, we present an extension of the structure-based approach termed site identification by ligand competitive saturation-biologics (SILCS-Biologics) to predict the effective charge of proteins. The SILCS-Biologics approach was applied on a range of protein targets in different salt environments for which membrane-confined electrophoresis-determined charges were previously reported. SILCS-Biologics maps the 3D distribution and predicted occupancy of ions, buffer molecules, and excipient molecules bound to the protein surface in a given salt environment. Using this information, the effective charge of the protein is predicted such that the concentrations of the ions and the presence of excipients or buffers are accounted for. Additionally, SILCS-Biologics also produces 3D structures of the binding sites of ions on the proteins, which enable further analyses such as the characterization of protein surface charge distribution and dipole moments in different environments. Notable is the capability of the method to account for competition between salts, excipients, and buffers on the calculated electrostatic properties in different protein formulations. Our study demonstrates the ability of the SILCS-Biologics approach to predict the effective charge of proteins and its applicability in uncovering protein-ion interactions and their contributions to protein solubility and function.
Collapse
Affiliation(s)
- Asuka A. Orr
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore, Baltimore, MD, USA
| | - Aoxiang Tao
- SilcsBio LLC, 1100 Wicomico Street, Suite 323, Baltimore, MD, USA
| | - Olgun Guvench
- SilcsBio LLC, 1100 Wicomico Street, Suite 323, Baltimore, MD, USA
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore, Baltimore, MD, USA
| |
Collapse
|
2
|
In silico identification of a β 2-adrenoceptor allosteric site that selectively augments canonical β 2AR-Gs signaling and function. Proc Natl Acad Sci U S A 2022; 119:e2214024119. [PMID: 36449547 PMCID: PMC9894167 DOI: 10.1073/pnas.2214024119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Activation of β2-adrenoceptors (β2ARs) causes airway smooth muscle (ASM) relaxation and bronchodilation, and β2AR agonists (β-agonists) are front-line treatments for asthma and other obstructive lung diseases. However, the therapeutic efficacy of β-agonists is limited by agonist-induced β2AR desensitization and noncanonical β2AR signaling involving β-arrestin that is shown to promote asthma pathophysiology. Accordingly, we undertook the identification of an allosteric site on β2AR that could modulate the activity of β-agonists to overcome these limitations. We employed the site identification by ligand competitive saturation (SILCS) computational method to comprehensively map the entire 3D structure of in silico-generated β2AR intermediate conformations and identified a putative allosteric binding site. Subsequent database screening using SILCS identified drug-like molecules with the potential to bind to the site. Experimental assays in HEK293 cells (expressing recombinant wild-type human β2AR) and human ASM cells (expressing endogenous β2AR) identified positive and negative allosteric modulators (PAMs and NAMs) of β2AR as assessed by regulation of β-agonist-stimulation of cyclic AMP generation. PAMs/NAMs had no effect on β-agonist-induced recruitment of β-arrestin to β2AR- or β-agonist-induced loss of cell surface expression in HEK293 cells expressing β2AR. Mutagenesis analysis of β2AR confirmed the SILCS identified site based on mutants of amino acids R131, Y219, and F282. Finally, functional studies revealed augmentation of β-agonist-induced relaxation of contracted human ASM cells and bronchodilation of contracted airways. These findings identify a allosteric binding site on the β2AR, whose activation selectively augments β-agonist-induced Gs signaling, and increases relaxation of ASM cells, the principal therapeutic effect of β-agonists.
Collapse
|
3
|
Effect of an Eco-Friendly Cuminaldehyde Guanylhydrazone Disinfectant on Shiga Toxin Production and Global Transcription of Escherichia coli. Toxins (Basel) 2022; 14:toxins14110752. [PMID: 36356001 PMCID: PMC9694190 DOI: 10.3390/toxins14110752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 10/24/2022] [Accepted: 10/30/2022] [Indexed: 11/06/2022] Open
Abstract
Antimicrobials have been important medicines used to treat various infections. However, some antibiotics increase the expression of Shiga toxin (Stx). Also, the pervasive use of persistent antibiotics has led to ecotoxicity and antibiotic resistance. In this study, a newly developed broad-spectrum and reversible antibiotic (guanylhydrazone disinfectant) was evaluated for its antibiotic activity and effects on Stx production and global transcription of bacteria. No Stx induction was observed in 25 Shiga toxin-producing E. coli (STEC) isolates treated with a sublethal concentration of the guanylhydrazone. A differential gene expression study comparing two guanylhydrazone-treated to non-treated E. coli strains indicated that the expression of a group of stress-responsive genes were enhanced. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that guanylhydrazone treatment significantly downregulated the pathways of ribosome and flagellar assembly in both pathogenic and non-pathogenic strains and differentially regulated some pathways essential for bacteria to maintain cell shape and gain survival advantage in two strains. In addition, upregulation of antibiotic resistant genes related to the multidrug efflux system and virulence genes coding for colibactin, colicin, and adhesin was observed in strains treated with the disinfectant. The knowledge obtained in this study contributes to our understanding of the mode of this disinfectant action and facilitates our effort to better use disinfectants for STEC treatments.
Collapse
|
4
|
Robinson EA, Frankenberg-Dinkel N, Xue F, Wilks A. Recombinant Production of Biliverdin IXβ and δ Isomers in the T7 Promoter Compatible Escherichia coli Nissle. Front Microbiol 2021; 12:787609. [PMID: 34956154 PMCID: PMC8692735 DOI: 10.3389/fmicb.2021.787609] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 11/11/2021] [Indexed: 11/23/2022] Open
Abstract
The ability to obtain purified biliverdin IX (BVIX) isomers other than the commercially available BVIXα is limited due to the low yields obtained by the chemical coupled oxidation of heme. Chemical oxidation requires toxic chemicals, has very poor BVIX yields (<0.05%), and is not conducive to scalable production. Alternative approaches utilizing recombinant E. coli BL21 expressing a cyanobacterial heme oxygenase have been employed for the production BVIXα, but yields are limited by the rate of endogenous heme biosynthesis. Furthermore, the emerging roles of BVIXβ and BVIXδ in biology and their lack of commercial availability has led to a need for an efficient and scalable method with the flexibility to produce all three physiologically relevant BVIX isomers. Herein, we have taken advantage of an optimized non-pathogenic E. coli Nissle (EcN(T7)) strain that encodes an endogenous heme transporter and an integrated T7 polymerase gene. Protein production of the Pseudomonas aeruginosa BVIXβ and BVIXδ selective heme oxygenase (HemO) or its BVIXα producing mutant (HemOα) in the EcN(T7) strain provides a scalable method to obtain all three isomers, that is not limited by the rate of endogenous heme biosynthesis, due to the natural ability of EcN(T7) to transport extracellular heme. Additionally, we have optimized our previous LC-MS/MS protocol for semi-preparative separation and validation of the BVIX isomers. Utilizing this new methodology for scalable production and separation we have increased the yields of the BVIXβ and -δ isomers >300-fold when compared to the chemical oxidation of heme.
Collapse
Affiliation(s)
- Elizabeth A. Robinson
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, United States
| | - Nicole Frankenberg-Dinkel
- Fachbereich Biologie, Abt. Mikrobiologie, Technische Universität Kaiserlautern, Kaiserslautern, Germany
| | - Fengtian Xue
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, United States
| | - Angela Wilks
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, United States
| |
Collapse
|
5
|
Extracellular haem utilization by the opportunistic pathogen Pseudomonas aeruginosa and its role in virulence and pathogenesis. Adv Microb Physiol 2021; 79:89-132. [PMID: 34836613 DOI: 10.1016/bs.ampbs.2021.07.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Iron is an essential micronutrient for all bacteria but presents a significant challenge given its limited bioavailability. Furthermore, iron's toxicity combined with the need to maintain iron levels within a narrow physiological range requires integrated systems to sense, regulate and transport a variety of iron complexes. Most bacteria encode systems to chelate and transport ferric iron (Fe3+) via siderophore receptor mediated uptake or via cytoplasmic energy dependent transport systems. Pathogenic bacteria have further lowered the barrier to iron acquisition by employing systems to utilize haem as a source of iron. Haem, a lipophilic and toxic molecule, presents a significant challenge for transport into the cell. As such pathogenic bacteria have evolved sophisticated cell surface signaling (CSS) and transport systems to sense and obtain haem from the host. Once internalized haem is cleaved by both oxidative and non-oxidative mechanisms to release iron. Herein we summarize our current understanding of the mechanism of haem sensing, uptake and utilization in Pseudomonas aeruginosa, its role in pathogenesis and virulence, and the potential of these systems as antimicrobial targets.
Collapse
|
6
|
Goel H, Hazel A, Ustach VD, Jo S, Yu W, MacKerell AD. Rapid and accurate estimation of protein-ligand relative binding affinities using site-identification by ligand competitive saturation. Chem Sci 2021; 12:8844-8858. [PMID: 34257885 PMCID: PMC8246086 DOI: 10.1039/d1sc01781k] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/24/2021] [Indexed: 01/18/2023] Open
Abstract
Predicting relative protein-ligand binding affinities is a central pillar of lead optimization efforts in structure-based drug design. The site identification by ligand competitive saturation (SILCS) methodology is based on functional group affinity patterns in the form of free energy maps that may be used to compute protein-ligand binding poses and affinities. Presented are results obtained from the SILCS methodology for a set of eight target proteins as reported originally in Wang et al. (J. Am. Chem. Soc., 2015, 137, 2695-2703) using free energy perturbation (FEP) methods in conjunction with enhanced sampling and cycle closure corrections. These eight targets have been subsequently studied by many other authors to compare the efficacy of their method while comparing with the outcomes of Wang et al. In this work, we present results for a total of 407 ligands on the eight targets and include specific analysis on the subset of 199 ligands considered previously. Using the SILCS methodology we can achieve an average accuracy of up to 77% and 74% when considering the eight targets with their 199 and 407 ligands, respectively, for rank-ordering ligand affinities as calculated by the percent correct metric. This accuracy increases to 82% and 80%, respectively, when the SILCS atomic free energy contributions are optimized using a Bayesian Markov-chain Monte Carlo approach. We also report other metrics including Pearson's correlation coefficient, Pearlman's predictive index, mean unsigned error, and root mean square error for both sets of ligands. The results obtained for the 199 ligands are compared with the outcomes of Wang et al. and other published works. Overall, the SILCS methodology yields similar or better-quality predictions without a priori need for known ligand orientations in terms of the different metrics when compared to current FEP approaches with significant computational savings while additionally offering quantitative estimates of individual atomic contributions to binding free energies. These results further validate the SILCS methodology as an accurate, computationally efficient tool to support lead optimization and drug discovery.
Collapse
Affiliation(s)
- Himanshu Goel
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy 20, Penn St. Baltimore Maryland 21201 USA +1-410-706-5017 +1-410-706-7442
| | - Anthony Hazel
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy 20, Penn St. Baltimore Maryland 21201 USA +1-410-706-5017 +1-410-706-7442
| | - Vincent D Ustach
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy 20, Penn St. Baltimore Maryland 21201 USA +1-410-706-5017 +1-410-706-7442
| | - Sunhwan Jo
- SilcsBio LLC 8 Market Place, Suite 300 Baltimore Maryland 21201 USA
| | - Wenbo Yu
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy 20, Penn St. Baltimore Maryland 21201 USA +1-410-706-5017 +1-410-706-7442
| | - Alexander D MacKerell
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy 20, Penn St. Baltimore Maryland 21201 USA +1-410-706-5017 +1-410-706-7442
- SilcsBio LLC 8 Market Place, Suite 300 Baltimore Maryland 21201 USA
| |
Collapse
|
7
|
Rekowski SP, Kroener BK, Kathuria D, Wani AA, Chourasiya SS, Conrad J, Bharatam PV, Frey W, Beifuss U. A novel copper-catalyzed, hydrazine-free synthesis of N-1 unsubstituted 1H-indazoles using stable guanylhydrazone salts as substrates. Tetrahedron 2021. [DOI: 10.1016/j.tet.2021.132192] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
8
|
Robinson EA, Wilks A, Xue F. Repurposing Acitretin as an Antipseudomonal Agent Targeting the Pseudomonas aeruginosa Iron-Regulated Heme Oxygenase. Biochemistry 2021; 60:689-698. [PMID: 33621054 DOI: 10.1021/acs.biochem.0c00895] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Iron is an essential micronutrient for the survival and virulence of the bacterial pathogen Pseudomonas aeruginosa. To overcome iron withholding and successfully colonize a host, P. aeruginosa uses a variety of mechanisms to acquire iron, including the secretion of high-affinity iron chelators (siderophores) or the uptake and utilization of heme. P. aeruginosa heme oxygenase (HemO) plays pivotal roles in heme sensing, uptake, and utilization and has emerged as a therapeutic target for the development of antipseudomonal agents. Using a high-throughput fluorescence quenching assay combined with minimum inhibitory concentration measurements, we screened the Selleck Bioactive collection of 2100 compounds and identified acitretin, a Food and Drug Administration-approved oral retinoid, as a potent and selective inhibitor of HemO. Acitretin binds to HemO with a KD value of 0.10 ± 0.02 μM and inhibits the growth of P. aeruginosa PAO1 with an IC50 of 70 ± 18 μg/mL. In addition, acitretin showed good selectivity for HemO, which uniquely generates BVIXβ/δ, over human heme oxygenase (hHO1) and other BVIXα-producing homologues such as the heme oxygenases from Neisseria meningitidis (nmHO) and Acinetobacter baumannii (abHO). The binding of acitretin within the HemO active site was confirmed by 1H-15N heteronuclear single-quantum coherence nuclear magnetic resonance, and molecular modeling provided further insight into potential interactions of acitretin with residues specific for orienting heme in the β/δ selective HemO. Moreover, at 20 μM, acitretin inhibited the enzymatic activity of HemO in P. aeruginosa cells by >60% and effectively blocked the ability of P. aeruginosa to sense and acquire heme as demonstrated in the β-galactosidase transcriptional reporter assay.
Collapse
Affiliation(s)
- Elizabeth A Robinson
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street, Baltimore, Maryland 21201, United States
| | - Angela Wilks
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street, Baltimore, Maryland 21201, United States
| | - Fengtian Xue
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street, Baltimore, Maryland 21201, United States
| |
Collapse
|
9
|
Soldano A, Yao H, Punchi Hewage AND, Meraz K, Annor-Gyamfi JK, Bunce RA, Battaile KP, Lovell S, Rivera M. Small Molecule Inhibitors of the Bacterioferritin (BfrB)-Ferredoxin (Bfd) Complex Kill Biofilm-Embedded Pseudomonas aeruginosa Cells. ACS Infect Dis 2021; 7:123-140. [PMID: 33269912 PMCID: PMC7802073 DOI: 10.1021/acsinfecdis.0c00669] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Indexed: 01/05/2023]
Abstract
Bacteria depend on a well-regulated iron homeostasis to survive adverse environments. A key component of the iron homeostasis machinery is the compartmentalization of Fe3+ in bacterioferritin and its subsequent mobilization as Fe2+ to satisfy metabolic requirements. In Pseudomonas aeruginosa Fe3+ is compartmentalized in bacterioferritin (BfrB), and its mobilization to the cytosol requires binding of a ferredoxin (Bfd) to reduce the stored Fe3+ and release the soluble Fe2+. Blocking the BfrB-Bfd complex in P. aeruginosa by deletion of the bfd gene triggers an irreversible accumulation of Fe3+ in BfrB, concomitant cytosolic iron deficiency and significant impairment of biofilm development. Herein we report that small molecules developed to bind BfrB at the Bfd binding site block the BfrB-Bfd complex, inhibit the mobilization of iron from BfrB in P. aeruginosa cells, elicit a bacteriostatic effect on planktonic cells, and are bactericidal to cells embedded in mature biofilms.
Collapse
Affiliation(s)
- Anabel Soldano
- Department
of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, Louisiana 70803, United States
| | - Huili Yao
- Department
of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, Louisiana 70803, United States
| | | | - Kevin Meraz
- Department
of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Joel K. Annor-Gyamfi
- Department
of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Richard A. Bunce
- Department
of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Kevin P. Battaile
- NYX, New York Structural Biology Center, Upton, New York 11973, United States
| | - Scott Lovell
- Protein
Structure Laboratory, University of Kansas, 2034 Becker Drive, Lawrence, Kansas 66047, United States
| | - Mario Rivera
- Department
of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, Louisiana 70803, United States
| |
Collapse
|
10
|
Fernández-Fierro A, Funes SC, Rios M, Covián C, González J, Kalergis AM. Immune Modulation by Inhibitors of the HO System. Int J Mol Sci 2020; 22:ijms22010294. [PMID: 33396647 PMCID: PMC7794909 DOI: 10.3390/ijms22010294] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 12/16/2020] [Accepted: 12/18/2020] [Indexed: 12/23/2022] Open
Abstract
The heme oxygenase (HO) system involves three isoforms of this enzyme, HO-1, HO-2, and HO-3. The three of them display the same catalytic activity, oxidating the heme group to produce biliverdin, ferrous iron, and carbon monoxide (CO). HO-1 is the isoform most widely studied in proinflammatory diseases because treatments that overexpress this enzyme promote the generation of anti-inflammatory products. However, neonatal jaundice (hyperbilirubinemia) derived from HO overexpression led to the development of inhibitors, such as those based on metaloproto- and meso-porphyrins inhibitors with competitive activity. Further, non-competitive inhibitors have also been identified, such as synthetic and natural imidazole-dioxolane-based, small synthetic molecules, inhibitors of the enzyme regulation pathway, and genetic engineering using iRNA or CRISPR cas9. Despite most of the applications of the HO inhibitors being related to metabolic diseases, the beneficial effects of these molecules in immune-mediated diseases have also emerged. Different medical implications, including cancer, Alzheimer´s disease, and infections, are discussed in this article and as to how the selective inhibition of HO isoforms may contribute to the treatment of these ailments.
Collapse
Affiliation(s)
- Ayleen Fernández-Fierro
- Millenium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331150 Santiago, Chile; (A.F.-F.); (M.R.); (C.C.); (J.G.)
| | - Samanta C. Funes
- Instituto Multidisciplinario de Investigaciones Biológicas-San Luis, Consejo Nacional de Investigaciones Científicas y Técnicas—Universidad Nacional de San Luis, 5700 San Luis, Argentina;
| | - Mariana Rios
- Millenium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331150 Santiago, Chile; (A.F.-F.); (M.R.); (C.C.); (J.G.)
| | - Camila Covián
- Millenium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331150 Santiago, Chile; (A.F.-F.); (M.R.); (C.C.); (J.G.)
| | - Jorge González
- Millenium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331150 Santiago, Chile; (A.F.-F.); (M.R.); (C.C.); (J.G.)
| | - Alexis M. Kalergis
- Millenium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331150 Santiago, Chile; (A.F.-F.); (M.R.); (C.C.); (J.G.)
- Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, 8331150 Santiago, Chile
- Correspondence: ; Tel.: +56-22-686-2842
| |
Collapse
|
11
|
Mousaei M, Kudaibergenova M, MacKerell AD, Noskov S. Assessing hERG1 Blockade from Bayesian Machine-Learning-Optimized Site Identification by Ligand Competitive Saturation Simulations. J Chem Inf Model 2020; 60:6489-6501. [PMID: 33196188 PMCID: PMC7839320 DOI: 10.1021/acs.jcim.0c01065] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Drug-induced cardiotoxicity is a potentially lethal and yet one of the most common side effects with the drugs in clinical use. Most of the drug-induced cardiotoxicity is associated with an off-target pharmacological blockade of K+ currents carried out by the cardiac Human-Ether-a-go-go-Related (hERG1) potassium channel. There is a compulsory preclinical stage safety assessment for the hERG1 blockade for all classes of drugs, which adds substantially to the cost of drug development. The availability of a high-resolution cryogenic electron microscopy (cryo-EM) structure for the channel in its open/depolarized state solved in 2017 enabled the application of molecular modeling for rapid assessment of drug blockade by molecular docking and simulation techniques. More importantly, if successful, in silico methods may allow a path to lead-compound salvaging by mapping out key block determinants. Here, we report the blind application of the site identification by the ligand competitive saturation (SILCS) protocol to map out druggable/regulatory hotspots in the hERG1 channel available for blockers and activators. The SILCS simulations use small solutes representative of common functional groups to sample the chemical space for the entire protein and its environment using all-atom simulations. The resulting chemical maps, FragMaps, explicitly account for receptor flexibility, protein-fragment interactions, and fragment desolvation penalty allowing for rapid ranking of potential ligands as blockers or nonblockers of hERG1. To illustrate the power of the approach, SILCS was applied to a test set of 55 blockers with diverse chemical scaffolds and pIC50 values measured under uniform conditions. The original SILCS model was based on the all-atom modeling of the hERG1 channel in an explicit lipid bilayer and was further augmented with a Bayesian-optimization/machine-learning (BML) stage employing an independent literature-derived training set of 163 molecules. BML approach was used to determine weighting factors for the FragMaps contributions to the scoring function. pIC50 predictions from the combined SILCS/BML approach to the 55 blockers showed a Pearson correlation (PC) coefficient of >0.535 relative to the experimental data. SILCS/BML model was shown to yield substantially improved performance as compared to commonly used rigid and flexible molecular docking methods for a well-established cohort of hERG1 blockers, where no correlation with experimental data was recorded. SILCS/BML results also suggest that a proper weighting of protonation states of common blockers present at physiological pH is essential for accurate predictions of blocker potency. The precalculated and optimized SILCS FragMaps can now be used for the rapid screening of small molecules for their cardiotoxic potential as well as for exploring alternative binding pockets in the hERG1 channel with applications to the rational design of activators.
Collapse
Affiliation(s)
- Mahdi Mousaei
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Meruyert Kudaibergenova
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Alexander D. MacKerell
- Computer-Aided Drug Design Center, Department of Pharmaceutical Science, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
| | - Sergei Noskov
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| |
Collapse
|
12
|
Abstract
Drug-resistant infections pose a significant risk to global health as pathogenic bacteria become increasingly difficult to treat. The rapid selection of resistant strains through poor antibiotic stewardship has reduced the number of viable treatments and increased morbidity of infections, especially among the immunocompromised. To circumvent such challenges, new strategies are required to stay ahead of emerging resistance trends, yet research and funding for antibiotic development lags other classes of therapeutics. Though the use of metals in therapeutics has been around for centuries, recent strategies have devoted a great deal of effort into the pathways through which bacteria acquire and utilize iron, which is critical for the establishment of infection. To target iron uptake systems, siderophore-drug conjugates have been developed that hijack siderophore-based iron uptake for delivery of antibiotics. While this strategy has produced several potential leads, the use of siderophores in infection is diminished over time when bacteria adapt to utilize heme as an iron source, leading to a need for the development of porphyrin mimetics as therapeutics. The use of such strategies as well as the inclusion of gallium, a redox-inert iron mimic, are herein reviewed.
Collapse
Affiliation(s)
- Garrick Centola
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, USA.
| | | | | |
Collapse
|
13
|
Mobilization of Iron Stored in Bacterioferritin Is Required for Metabolic Homeostasis in Pseudomonas aeruginosa. Pathogens 2020; 9:pathogens9120980. [PMID: 33255203 PMCID: PMC7760384 DOI: 10.3390/pathogens9120980] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/22/2020] [Accepted: 11/23/2020] [Indexed: 12/12/2022] Open
Abstract
Iron homeostasis offers a significant bacterial vulnerability because pathogens obtain essential iron from their mammalian hosts, but host-defenses maintain vanishingly low levels of free iron. Although pathogens have evolved mechanisms to procure host-iron, these depend on well-regulated iron homeostasis. To disrupt iron homeostasis, our work has targeted iron mobilization from the iron storage protein bacterioferritin (BfrB) by blocking a required interaction with its cognate ferredoxin partner (Bfd). The blockade of the BfrB–Bfd complex by deletion of the bfd gene (Δbfd) causes iron to irreversibly accumulate in BfrB. In this study we used mass spectrometry and NMR spectroscopy to compare the proteomic response and the levels of key intracellular metabolites between wild type (wt) and isogenic ΔbfdP. aeruginosa strains. We find that the irreversible accumulation of unusable iron in BfrB leads to acute intracellular iron limitation, even if the culture media is iron-sufficient. Importantly, the iron limitation and concomitant iron metabolism dysregulation trigger a cascade of events that lead to broader metabolic homeostasis disruption, which includes sulfur limitation, phenazine-mediated oxidative stress, suboptimal amino acid synthesis and altered carbon metabolism.
Collapse
|
14
|
MacKerell AD, Jo S, Lakkaraju SK, Lind C, Yu W. Identification and characterization of fragment binding sites for allosteric ligand design using the site identification by ligand competitive saturation hotspots approach (SILCS-Hotspots). Biochim Biophys Acta Gen Subj 2020; 1864:129519. [PMID: 31911242 DOI: 10.1016/j.bbagen.2020.129519] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/21/2019] [Accepted: 12/31/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND Fragment-based ligand design is used for the development of novel ligands that target macromolecules, most notably proteins. Central to its success is the identification of fragment binding sites that are spatially adjacent such that fragments occupying those sites may be linked to create drug-like ligands. Current experimental and computational approaches that address this problem typically identify only a limited number of sites as well as use a limited number of fragment types. METHODS The site-identification by ligand competitive saturation (SILCS) approach is extended to the identification of fragment bindings sites, with the method termed SILCS-Hotspots. The approach involves precomputation of the SILCS FragMaps following which the identification of Hotspots, performed by identifying of all possible fragment binding sites on the full 3D structure of the protein followed by spatial clustering. RESULTS The SILCS-Hotspots approach identifies a large number of sites on the target protein, including many sites not accessible in experimental structures due to low binding affinities and binding sites on the protein interior. The identified sites are shown to recapitulate the location of known drug-like molecules in both allosteric and orthosteric binding sites on seven proteins including the androgen receptor, the CDK2 and Erk5 kinases, PTP1B phosphatase and three GPCRs; the β2-adrenergic, GPR40 fatty-acid binding and M2-muscarinic receptors. Analysis indicates the importance of considering all possible fragment binding sites, and not just those accessible to experimental methods, when identifying novel binding sites and performing ligand design versus just considering the most favorable sites. The approach is shown to identify a larger number of known binding sites of drug-like molecules versus the commonly used FTMap and Fpocket methods. GENERAL SIGNIFICANCE The present results indicate the potential utility of the SILCS-Hotspots approach for fragment-based rational design of ligands, including allosteric modulators.
Collapse
Affiliation(s)
- Alexander D MacKerell
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201, United States of America.
| | - Sunhwan Jo
- SilcsBio, LLC, 8 Market Place, Suite 300, Baltimore, MD 21202, United States of America
| | | | - Christoffer Lind
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201, United States of America
| | - Wenbo Yu
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201, United States of America
| |
Collapse
|
15
|
Božinović N, Ajdačić V, Lazic J, Lecerf M, Daventure V, Nikodinovic-Runic J, Opsenica IM, Dimitrov JD. Aromatic Guanylhydrazones for the Control of Heme-Induced Antibody Polyreactivity. ACS OMEGA 2019; 4:20450-20458. [PMID: 31858028 PMCID: PMC6906781 DOI: 10.1021/acsomega.9b01548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 08/06/2019] [Indexed: 06/10/2023]
Abstract
In a healthy immune repertoire, there exists a fraction of polyreactive antibodies that can bind to a variety of unrelated self- and foreign antigens. Apart from naturally polyreactive antibodies, in every healthy individual, there is a fraction of antibody that can gain polyreactivity upon exposure to porphyrin cofactor heme. Molecular mechanisms and biological significance of the appearance of cryptic polyreactivity are not well understood. It is believed that heme acts as an interfacial cofactor between the antibody and the newly recognized antigens. To further test this claim and gain insight into the types of interactions involved in heme binding, we herein investigated the influence of a group of aromatic guanylhydrazone molecules on the heme-induced antibody polyreactivity. From the analysis of SAR and the results of UV-vis absorbance spectroscopy, it was concluded that the most probable mechanism by which the studied molecules inhibit heme-mediated polyreactivity of the antibody is the direct binding to heme, thus preventing heme from binding to antibody and/or antigen. The inhibitory capacity of the most potent compounds was substantially higher than that of chloroquine, a well-known heme binder. Some of the guanylhydrazone molecules were able to induce polyreactivity of the studied antibody themselves, possibly by a mechanism similar to heme. Results described here point to the conclusion that heme indeed must bind to an antibody to induce its polyreactivity, and that both π-stacking interactions and iron coordination contribute to the binding affinity, while certain structures, such as guanylhydrazones, can interfere with these processes.
Collapse
Affiliation(s)
- Nina Božinović
- Centre
de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC,
Université Paris Descartes, Université Paris Diderot, F-75006 Paris, France
| | - Vladimir Ajdačić
- University
of Belgrade—Faculty of Chemistry, Studentski trg 16, P.O. Box 51, 11158 Belgrade, Serbia
| | - Jelena Lazic
- University
of Belgrade—Faculty of Chemistry, Studentski trg 16, P.O. Box 51, 11158 Belgrade, Serbia
| | - Maxime Lecerf
- Centre
de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC,
Université Paris Descartes, Université Paris Diderot, F-75006 Paris, France
| | - Victoria Daventure
- Centre
de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC,
Université Paris Descartes, Université Paris Diderot, F-75006 Paris, France
| | - Jasmina Nikodinovic-Runic
- University
of Belgrade—Faculty of Chemistry, Studentski trg 16, P.O. Box 51, 11158 Belgrade, Serbia
- Institute
of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11000 Belgrade, Serbia
| | - Igor M. Opsenica
- University
of Belgrade—Faculty of Chemistry, Studentski trg 16, P.O. Box 51, 11158 Belgrade, Serbia
| | - Jordan D. Dimitrov
- Centre
de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC,
Université Paris Descartes, Université Paris Diderot, F-75006 Paris, France
| |
Collapse
|
16
|
Krishna MS, Wang Z, Zheng L, Bowry J, Ong AAL, Mu Y, Prabakaran M, Chen G. Incorporating G-C Pair-Recognizing Guanidinium into PNAs for Sequence and Structure Specific Recognition of dsRNAs over dsDNAs and ssRNAs. Biochemistry 2019; 58:3777-3788. [PMID: 31424191 DOI: 10.1021/acs.biochem.9b00608] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Recognition of RNAs under physiological conditions is important for the development of chemical probes and therapeutic ligands. Nucleobase-modified dsRNA-binding PNAs (dbPNAs) are promising for the recognition of dsRNAs in a sequence and structure specific manner under near-physiological conditions. Guanidinium is often present in proteins and small molecules for the recognition of G bases in nucleic acids, in cell-penetrating carriers, and in bioactive drug molecules, which might be due to the fact that guanidinium is amphiphilic and has unique hydrogen bonding and stacking properties. We hypothesized that a simple guanidinium moiety can be directly incorporated into PNAs to facilitate enhanced molecular recognition of G-C pairs in dsRNAs and improved bioactivity. We grafted a guanidinium moiety directly into a PNA monomer (designated as R) using a two-carbon linker as guided by computational modeling studies. The synthetic scheme of the PNA R monomer is relatively simple compared to that of the previously reported L monomer. We incorporated the R residue into various dbPNAs for binding studies. dbPNAs incorporated with R residues are excellent in sequence specifically recognizing G-C pairs in dsRNAs over dsDNA and ssRNAs. We demonstrated that the R residue is compatible with unmodified T and C and previously developed modified L and Q residues in dbPNAs for targeting model dsRNAs, the influenza A viral panhandle duplex structure, and the HIV-1 frameshift site RNA hairpin. Furthermore, R residues enhance the cellular uptake of PNAs.
Collapse
Affiliation(s)
- Manchugondanahalli S Krishna
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Zhenzhang Wang
- Temasek Life Science Laboratory, 1 Research Link, National University of Singapore , Singapore 117604
| | - Liangzhen Zheng
- School of Biological Sciences , Nanyang Technological University , Singapore 637551
| | - Jogesh Bowry
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371.,Department of Chemistry , University of Southampton , Southampton SO17 1BJ , U.K
| | - Alan Ann Lerk Ong
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Yuguang Mu
- School of Biological Sciences , Nanyang Technological University , Singapore 637551
| | - Mookkan Prabakaran
- Temasek Life Science Laboratory, 1 Research Link, National University of Singapore , Singapore 117604
| | - Gang Chen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| |
Collapse
|
17
|
Giardina BJ, Shahzad S, Huang W, Wilks A. Heme uptake and utilization by hypervirulent Acinetobacter baumannii LAC-4 is dependent on a canonical heme oxygenase (abHemO). Arch Biochem Biophys 2019; 672:108066. [PMID: 31398314 DOI: 10.1016/j.abb.2019.108066] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 08/02/2019] [Accepted: 08/06/2019] [Indexed: 02/06/2023]
Abstract
Acinetobacter baumannii is an opportunistic pathogen that causes serious infections in critically ill and immune compromised patients. The ability to acquire iron from the hosts iron and heme containing proteins is critical to their survival and virulence. The majority of A. baumannii hypervirulent strains encode a heme uptake system that includes a putative heme oxygenase (hemO). Despite reports indicating A. baumannii can grow on heme direct evidence of extracellular heme uptake and metabolism has not been shown. Through isotopic labeling (13C-heme) we show the hypervirulent A. baumannii LAC-4 metabolizes heme to biliverdin IXα (BVIXα), whereas ATC 17978 that lacks the hemO gene cluster cannot efficiently utilize heme. Expression and purification of the protein encoded by the A. baumannii LAC-4 hemO gene confirmed catalytic conversion of heme to BVIX. We further show inhibition of abHemO with previously characterized P. aeruginosa HemO inhibitors in a fluorescence based assay that couples HemO catalytic activity to the BVIXα binding phytochrome IFP1.4. Furthermore, the hemO gene cluster encodes genes with homology to heme-dependent extra cytoplasmic function (ECF) σ factor systems. The hemophore-dependent ECF system in Pseudomonas aeruginosa has been shown to play a critical role in heme sensing and virulence within the host. The prevalence of a hemO gene cluster in A. baumannii LAC4 and other hypervirulent strains suggests it is required within the host to adapt and utilize heme and is a major contributor to virulence.
Collapse
Affiliation(s)
- Bennett J Giardina
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, 21201, USA
| | - Saba Shahzad
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, 21201, USA
| | - Weiliang Huang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, 21201, USA
| | - Angela Wilks
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, 21201, USA.
| |
Collapse
|
18
|
Ustach VD, Lakkaraju SK, Jo S, Yu W, Jiang W, MacKerell AD. Optimization and Evaluation of Site-Identification by Ligand Competitive Saturation (SILCS) as a Tool for Target-Based Ligand Optimization. J Chem Inf Model 2019; 59:3018-3035. [PMID: 31034213 PMCID: PMC6597307 DOI: 10.1021/acs.jcim.9b00210] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Chemical fragment cosolvent sampling techniques have become a versatile tool in ligand-protein binding prediction. Site-identification by ligand competitive saturation (SILCS) is one such method that maps the distribution of chemical fragments on a protein as free energy fields called FragMaps. Ligands are then simulated via Monte Carlo techniques in the field of the FragMaps (SILCS-MC) to predict their binding conformations and relative affinities for the target protein. Application of SILCS-MC using a number of different scoring schemes and MC sampling protocols against multiple protein targets was undertaken to evaluate and optimize the predictive capability of the method. Seven protein targets and 551 ligands with broad chemical variability were used to evaluate and optimize the model to maximize Pearson's correlation coefficient, Pearlman's predictive index, correct relative binding affinity, and root-mean-square error versus the absolute experimental binding affinities. Across the protein-ligand sets, the relative affinities of the ligands were predicted correctly an average of 69% of the time for the highest overall SILCS protocol. Training the FragMap weighting factors using a Bayesian machine learning (ML) algorithm led to an increase to an average 75% relative correct affinity predictions. Furthermore, once the optimal protocol is identified for a specific protein-ligand system average predictabilities of 76% are achieved. The ML algorithm is successful with small training sets of data (30 or more compounds) due to the use of physically correct FragMap weights as priors. Notably, the 76% correct relative prediction rate is similar to or better than free energy perturbation methods that are significantly computationally more expensive than SILCS. The results further support the utility of SILCS as a powerful and computationally accessible tool to support lead optimization and development in drug discovery.
Collapse
Affiliation(s)
- Vincent D. Ustach
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201
| | | | - Sunhwan Jo
- SilcsBio, LLC, 8 Market Place, Suite 300, Baltimore, MD 21202
| | - Wenbo Yu
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201
| | - Wenjuan Jiang
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201
| | - Alexander D. MacKerell
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201
- SilcsBio, LLC, 8 Market Place, Suite 300, Baltimore, MD 21202
| |
Collapse
|
19
|
Hunsaker EW, Franz KJ. Emerging Opportunities To Manipulate Metal Trafficking for Therapeutic Benefit. Inorg Chem 2019; 58:13528-13545. [PMID: 31247859 DOI: 10.1021/acs.inorgchem.9b01029] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The indispensable requirement for metals in life processes has led to the evolution of sophisticated mechanisms that allow organisms to maintain dynamic equilibria of these ions. This dynamic control of the level, speciation, and availability of a variety of metal ions allows organisms to sustain biological processes while avoiding toxicity. When functioning properly, these mechanisms allow cells to return to their metal homeostatic set points following shifts in the metal availability or other stressors. These periods of transition, when cells are in a state of flux in which they work to regain homeostasis, present windows of opportunity to pharmacologically manipulate targets associated with metal-trafficking pathways in ways that could either facilitate a return to homeostasis and the recovery of cellular function or further push cells outside of homeostasis and into cellular distress. The purpose of this Viewpoint is to highlight emerging opportunities for chemists and chemical biologists to develop compounds to manipulate metal-trafficking processes for therapeutic benefit.
Collapse
Affiliation(s)
- Elizabeth W Hunsaker
- Department of Chemistry , Duke University , French Family Science Center, 124 Science Drive , Durham , North Carolina 27708 , United States
| | - Katherine J Franz
- Department of Chemistry , Duke University , French Family Science Center, 124 Science Drive , Durham , North Carolina 27708 , United States
| |
Collapse
|
20
|
Punchi Hewage AND, Yao H, Nammalwar B, Gnanasekaran KK, Lovell S, Bunce RA, Eshelman K, Phaniraj SM, Lee MM, Peterson BR, Battaile KP, Reitz AB, Rivera M. Small Molecule Inhibitors of the BfrB-Bfd Interaction Decrease Pseudomonas aeruginosa Fitness and Potentiate Fluoroquinolone Activity. J Am Chem Soc 2019; 141:8171-8184. [PMID: 31038945 PMCID: PMC6535718 DOI: 10.1021/jacs.9b00394] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
The iron storage
protein bacterioferritin (BfrB) is central to
bacterial iron homeostasis. The mobilization of iron from BfrB, which
requires binding by a cognate ferredoxin (Bfd), is essential to the
regulation of cytosolic iron levels in P. aeruginosa. This paper describes the structure-guided development of small
molecule inhibitors of the BfrB–Bfd protein–protein
interaction. The process was initiated by screening a fragment library
and followed by obtaining the structure of a fragment hit bound to
BfrB. The structural insights were used to develop a series of 4-(benzylamino)-
and 4-((3-phenylpropyl)amino)-isoindoline-1,3-dione analogs that selectively
bind BfrB at the Bfd binding site. Challenging P. aeruginosa cells with the 4-substituted isoindoline analogs revealed a dose-dependent
growth phenotype. Further investigation determined that the analogs
elicit a pyoverdin hyperproduction phenotype that is consistent with
blockade of the BfrB–Bfd interaction and ensuing irreversible
accumulation of iron in BfrB, with concomitant depletion of iron in
the cytosol. The irreversible accumulation of iron in BfrB prompted
by the 4-substituted isoindoline analogs was confirmed by visualization
of BfrB-iron in P. aeruginosa cell lysates separated
on native PAGE gels and stained for iron with Ferene S. Challenging P. aeruginosa cultures with a combination of commercial
fluoroquinolone and our isoindoline analogs results in significantly
lower cell survival relative to treatment with either antibiotic or
analog alone. Collectively, these findings furnish proof of concept
for the usefulness of small molecule probes designed to dysregulate
bacterial iron homeostasis by targeting a protein–protein interaction
pivotal for iron storage in the bacterial cell.
Collapse
Affiliation(s)
- Achala N D Punchi Hewage
- Department of Chemistry , University of Kansas , 2030 Becker Drive , Lawrence , Kansas 66047 , United States
| | - Huili Yao
- Department of Chemistry , Louisiana State University , 229A Choppin Hall , Baton Rouge , Louisiana 70803 , United States
| | - Baskar Nammalwar
- Department of Chemistry , Oklahoma State University , Stillwater , Oklahoma 74078 , United States
| | | | - Scott Lovell
- Protein Structure Laboratory , University of Kansas , 2034 Becker Drive , Lawrence , Kansas 66047 , United States
| | - Richard A Bunce
- Department of Chemistry , Oklahoma State University , Stillwater , Oklahoma 74078 , United States
| | - Kate Eshelman
- Department of Chemistry , University of Kansas , 2030 Becker Drive , Lawrence , Kansas 66047 , United States
| | - Sahishna M Phaniraj
- Department of Medicinal Chemistry , University of Kansas , 2034 Becker Drive , Lawrence , Kansas 66047 , United States
| | - Molly M Lee
- Department of Medicinal Chemistry , University of Kansas , 2034 Becker Drive , Lawrence , Kansas 66047 , United States
| | - Blake R Peterson
- Department of Medicinal Chemistry , University of Kansas , 2034 Becker Drive , Lawrence , Kansas 66047 , United States
| | - Kevin P Battaile
- IMCA-CAT , Hauptman Woodward Medical Research Institute , 9700 South Cass Avenue, Building 435A , Argonne , Illinois 60439 , United States
| | - Allen B Reitz
- Fox Chase Chemical Diversity Center, Inc. , 3805 Old Easton Road , Doylestown , Pennsylvania 18902 , United States
| | - Mario Rivera
- Department of Chemistry , Louisiana State University , 229A Choppin Hall , Baton Rouge , Louisiana 70803 , United States
| |
Collapse
|
21
|
The effects of novel heme oxygenase inhibitors on the growth of Pseudomonas aeruginosa. Microb Pathog 2019; 129:64-67. [DOI: 10.1016/j.micpath.2019.01.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/19/2018] [Accepted: 01/30/2019] [Indexed: 11/24/2022]
|
22
|
Yu W, Jo S, Lakkaraju SK, Weber DJ, MacKerell AD. Exploring protein-protein interactions using the site-identification by ligand competitive saturation methodology. Proteins 2019; 87:289-301. [PMID: 30582220 DOI: 10.1002/prot.25650] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 12/06/2018] [Accepted: 12/19/2018] [Indexed: 01/05/2023]
Abstract
Protein docking methods are powerful computational tools to study protein-protein interactions (PPI). While a significant number of docking algorithms have been developed, they are usually based on rigid protein models or with limited considerations of protein flexibility and the desolvation effect is rarely considered in docking energy functions, which may lower the accuracy of the predictions. To address these issues, we introduce a PPI energy function based on the site-identification by ligand competitive saturation (SILCS) framework and utilize the fast Fourier transform (FFT) correlation approach. The free energy content of the SILCS FragMaps represent an alternative to traditional energy grids and they can be efficiently utilized to guide FFT-based protein docking. Application of the approach to eight diverse test cases, including seven from Protein Docking Benchmark 5.0, showed the PPI prediction using SILCS approach (SILCS-PPI) to be competitive with several commonly used protein docking methods indicating that the method has the ability to both qualitatively and quantitatively inform the prediction of PPI. Results show the utility of the SILCS-PPI docking approach for determination of probability distributions of PPI interactions over the surface of both partner proteins, allowing for identification of alternate binding poses. Such binding poses are confirmed by experimental crystal contacts in our test cases. While more computationally demanding than available PPI docking technologies, we anticipate that the SILCS-PPI docking approach will offer an alternative methodology for improved evaluation of PPIs that could be used in a variety of fields from systems biology to excipient design for biologics-based drugs.
Collapse
Affiliation(s)
- Wenbo Yu
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland.,Institute for Bioscience and Biotechnology Research (IBBR), Rockville, Maryland.,Center for Biomolecular Therapeutics (CBT), School of Medicine, University of Maryland, Baltimore, Maryland
| | | | | | - David J Weber
- Institute for Bioscience and Biotechnology Research (IBBR), Rockville, Maryland.,Center for Biomolecular Therapeutics (CBT), School of Medicine, University of Maryland, Baltimore, Maryland
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland.,Institute for Bioscience and Biotechnology Research (IBBR), Rockville, Maryland.,Center for Biomolecular Therapeutics (CBT), School of Medicine, University of Maryland, Baltimore, Maryland.,SilcsBio LLC, Baltimore, Maryland
| |
Collapse
|
23
|
Chourasiya SS, Kathuria D, Wani AA, Bharatam PV. Azines: synthesis, structure, electronic structure and their applications. Org Biomol Chem 2019; 17:8486-8521. [DOI: 10.1039/c9ob01272a] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Azines (2,3-diaza-1,3-butadienes): structure, electronic structure, tautomerism, and their applications in organic synthesis, medicinal chemistry and materials chemistry.
Collapse
Affiliation(s)
- Sumit S. Chourasiya
- Department of Medicinal Chemistry
- National Institute of Pharmaceutical Education and Research (NIPER)
- India
| | - Deepika Kathuria
- Department of Medicinal Chemistry
- National Institute of Pharmaceutical Education and Research (NIPER)
- India
| | - Aabid Abdullah Wani
- Department of Medicinal Chemistry
- National Institute of Pharmaceutical Education and Research (NIPER)
- India
| | - Prasad V. Bharatam
- Department of Medicinal Chemistry
- National Institute of Pharmaceutical Education and Research (NIPER)
- India
| |
Collapse
|
24
|
Cheng H, Linhares BM, Yu W, Cardenas MG, Ai Y, Jiang W, Winkler A, Cohen S, Melnick A, MacKerell A, Cierpicki T, Xue F. Identification of Thiourea-Based Inhibitors of the B-Cell Lymphoma 6 BTB Domain via NMR-Based Fragment Screening and Computer-Aided Drug Design. J Med Chem 2018; 61:7573-7588. [PMID: 29969259 PMCID: PMC6334293 DOI: 10.1021/acs.jmedchem.8b00040] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Protein-protein interactions (PPI) between the transcriptional repressor B-cell lymphoma 6 (BCL6) BTB domain (BCL6BTB) and its corepressors have emerged as a promising target for anticancer therapeutics. However, identification of potent, drug-like inhibitors of BCL6BTB has remained challenging. Using NMR-based screening of a library of fragment-like small molecules, we have identified a thiourea compound (7CC5) that binds to BCL6BTB. From this hit, the application of computer-aided drug design (CADD), medicinal chemistry, NMR spectroscopy, and X-ray crystallography has yielded an inhibitor, 15f, that demonstrated over 100-fold improved potency for BCL6BTB. This gain in potency was achieved by a unique binding mode that mimics the binding mode of the corepressor SMRT in the aromatic and the HDCH sites. The structure-activity relationship based on these new inhibitors will have a significant impact on the rational design of novel BCL6 inhibitors, facilitating the identification of therapeutics for the treatment of BCL6-dependent tumors.
Collapse
Affiliation(s)
- Huimin Cheng
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, Baltimore, Maryland, 21201, USA
| | - Brian M. Linhares
- University of Michigan, Department of Pathology, Ann Arbor, Michigan, 48109, USA
| | - Wenbo Yu
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, Baltimore, Maryland, 21201, USA,University of Maryland Computer-Aided Drug Design Center, Baltimore, Maryland, 21201, USA
| | - Mariano G. Cardenas
- Weill Cornell Medical College, Department of Hematology/Oncology, New York, New York, 10021, USA
| | - Yong Ai
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, Baltimore, Maryland, 21201, USA
| | - Wenjuan Jiang
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, Baltimore, Maryland, 21201, USA,University of Maryland Computer-Aided Drug Design Center, Baltimore, Maryland, 21201, USA
| | - Alyssa Winkler
- University of Michigan, Department of Pathology, Ann Arbor, Michigan, 48109, USA
| | - Sandra Cohen
- Weill Cornell Medical College, Department of Hematology/Oncology, New York, New York, 10021, USA
| | - Ari Melnick
- Weill Cornell Medical College, Department of Hematology/Oncology, New York, New York, 10021, USA
| | - Alexander MacKerell
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, Baltimore, Maryland, 21201, USA,University of Maryland Computer-Aided Drug Design Center, Baltimore, Maryland, 21201, USA
| | - Tomasz Cierpicki
- University of Michigan, Department of Pathology, Ann Arbor, Michigan, 48109, USA,Correspondence to: Professor Fengtian Xue at the Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street, Baltimore, Maryland 21201, USA, Phone: 410-706-8521, , Professor Tomasz Cierpicki at the University of Michigan, Department of Pathology, Ann Arbor, Michigan 48109, USA, Phone: 734-615-9324,
| | - Fengtian Xue
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, Baltimore, Maryland, 21201, USA,University of Maryland Computer-Aided Drug Design Center, Baltimore, Maryland, 21201, USA,Correspondence to: Professor Fengtian Xue at the Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street, Baltimore, Maryland 21201, USA, Phone: 410-706-8521, , Professor Tomasz Cierpicki at the University of Michigan, Department of Pathology, Ann Arbor, Michigan 48109, USA, Phone: 734-615-9324,
| |
Collapse
|
25
|
The Asp99-Arg188 salt bridge of the Pseudomonas aeruginosa HemO is critical in allowing conformational flexibility during catalysis. J Biol Inorg Chem 2018; 23:1057-1070. [PMID: 30194537 DOI: 10.1007/s00775-018-1609-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 08/23/2018] [Indexed: 12/17/2022]
Abstract
The P. aeruginosa iron-regulated heme oxygenase (HemO) is required within the host for the utilization of heme as an iron source. As iron is essential for survival and virulence, HemO represents a novel antimicrobial target. We recently characterized small molecule inhibitors that bind to an allosteric site distant from the heme pocket, and further proposed binding at this site disrupts a nearby salt bridge between D99 and R188. Herein, through a combination of site-directed mutagenesis and hydrogen-deuterium exchange mass spectrometry (HDX-MS), we determined that the disruption of the D99-R188 salt bridge leads to significant decrease in conformational flexibility within the distal and proximal helices that form the heme-binding site. The RR spectra of the resting state Fe(III) and reduced Fe(II)-deoxy heme-HemO D99A, R188A and D99/R188A complexes are virtually identical to those of wild-type HemO, indicating no significant change in the heme environment. Furthermore, mutation of D99 or R188 leads to a modest decrease in the stability of the Fe(II)-O2 heme complex. Despite this slight difference in Fe(II)-O2 stability, we observe complete loss of enzymatic activity. We conclude the loss of activity is a result of decreased conformational flexibility in helices previously shown to be critical in accommodating variation in the distal ligand and the resulting chemical intermediates generated during catalysis. Furthermore, this newly identified allosteric binding site on HemO represents a novel alternative drug-design strategy to that of competitive inhibition at the active site or via direct coordination of ligands to the heme iron.
Collapse
|
26
|
Conger MA, Pokhrel D, Liptak MD. Tight binding of heme to Staphylococcus aureus IsdG and IsdI precludes design of a competitive inhibitor. Metallomics 2018; 9:556-563. [PMID: 28401968 DOI: 10.1039/c7mt00035a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The micromolar equilibrium constants for heme dissociation from IsdG and IsdI reported in the literature call into question whether these enzymes are actually members of the iron-regulated surface determinant system of Staphylococcus aureus, which harvests heme iron from a host during infection. In order to address this question, the heme dissociation constants for IsdG and IsdI were reevaluated using three approaches. The heme dissociation equilibrium constants were measured using a UV/Vis absorption-detected assay analyzed with an assumption-free model, and using a newly developed fluorescence-detected assay. The heme dissociation rate constants were estimated using apomyoglobin competition assays. Analyses of the UV/Vis absorption data revealed a critical flaw in the previous measurements; heme is 99.9% protein-bound at the micromolar concentrations needed for UV/Vis absorption spectroscopy, which renders accurate equilibrium constant measurement nearly impossible. However, fluorescence can be measured for more dilute samples, and analyses of these data resulted in dissociation equilibrium constants of 1.4 ± 0.6 nM and 12.9 ± 1.3 nM for IsdG and IsdI, respectively. Analyses of the kinetic data obtained from apomyoglobin competition assays estimated heme dissociation rate constants of 0.022 ± 0.002 s-1 for IsdG and 0.092 ± 0.008 s-1 for IsdI. Based upon these data, and what is known regarding the post-translational regulation of IsdG and IsdI, it is proposed that only IsdG is a member of the heme iron acquisition pathway and IsdI regulates heme homeostasis. Furthermore, the nanomolar dissociation constants mean that heme is bound tightly by IsdG and indicates that competitive inhibition of this protein will be difficult. Instead, uncompetitive inhibition based upon a detailed understanding of enzyme mechanism is a more promising antibiotic development strategy.
Collapse
Affiliation(s)
- Matthew A Conger
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, USA.
| | | | | |
Collapse
|
27
|
Liang D, Robinson E, Hom K, Yu W, Nguyen N, Li Y, Zong Q, Wilks A, Xue F. Structure-based design and biological evaluation of inhibitors of the pseudomonas aeruginosa heme oxygenase (pa-HemO). Bioorg Med Chem Lett 2018; 28:1024-1029. [PMID: 29459206 DOI: 10.1016/j.bmcl.2018.02.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 02/03/2018] [Accepted: 02/13/2018] [Indexed: 02/03/2023]
Affiliation(s)
- Dongdong Liang
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, United States
| | - Elizabeth Robinson
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, United States
| | - Kellie Hom
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, United States
| | - Wenbo Yu
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, United States
| | - Nam Nguyen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, United States
| | - Yue Li
- Department of Chemistry and Biochemistry, University of Maryland College Park, College Park 20740, United States
| | - Qianshou Zong
- College of Biological and Chemical Sciences and Engineering, Jiaxing University, Jiaxing City, Zhejiang 314001, People's Republic of China
| | - Angela Wilks
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, United States.
| | - Fengtian Xue
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, United States.
| |
Collapse
|
28
|
Soldano A, Klinke S, Otero LH, Rivera M, Catalano-Dupuy DL, Ceccarelli EA. Structural and mutational analyses of the Leptospira interrogans virulence-related heme oxygenase provide insights into its catalytic mechanism. PLoS One 2017; 12:e0182535. [PMID: 28771589 PMCID: PMC5542595 DOI: 10.1371/journal.pone.0182535] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 07/19/2017] [Indexed: 11/25/2022] Open
Abstract
Heme oxygenase from Leptospira interrogans is an important virulence factor. During catalysis, redox equivalents are provided to this enzyme by the plastidic-type ferredoxin-NADP+ reductase also found in L. interrogans. This process may have evolved to aid this bacterial pathogen to obtain heme-iron from their host and enable successful colonization. Herein we report the crystal structure of the heme oxygenase-heme complex at 1.73 Å resolution. The structure reveals several distinctive features related to its function. A hydrogen bonded network of structural water molecules that extends from the catalytic site to the protein surface was cleared observed. A depression on the surface appears to be the H+ network entrance from the aqueous environment to the catalytic site for O2 activation, a key step in the heme oxygenase reaction. We have performed a mutational analysis of the F157, located at the above-mentioned depression. The mutant enzymes were unable to carry out the complete degradation of heme to biliverdin since the reaction was arrested at the verdoheme stage. We also observed that the stability of the oxyferrous complex, the efficiency of heme hydroxylation and the subsequent conversion to verdoheme was adversely affected. These findings underscore a long-range communication between the outer fringes of the hydrogen-bonded network of structural waters and the heme active site during catalysis. Finally, by analyzing the crystal structures of ferredoxin-NADP+ reductase and heme oxygenase, we propose a model for the productive association of these proteins.
Collapse
Affiliation(s)
- Anabel Soldano
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Sebastián Klinke
- Fundación Instituto Leloir, IIBBA-CONICET, and Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Buenos Aires, Argentina
| | - Lisandro H. Otero
- Fundación Instituto Leloir, IIBBA-CONICET, and Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Buenos Aires, Argentina
| | - Mario Rivera
- Department of Chemistry and Ralph N. Adams Institute for Bioanalytical Chemistry, University of Kansas, Lawrence, Kansas, United States of America
| | - Daniela L. Catalano-Dupuy
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Eduardo A. Ceccarelli
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
- * E-mail:
| |
Collapse
|
29
|
Brewitz HH, Hagelueken G, Imhof D. Structural and functional diversity of transient heme binding to bacterial proteins. Biochim Biophys Acta Gen Subj 2017; 1861:683-697. [DOI: 10.1016/j.bbagen.2016.12.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 12/15/2016] [Accepted: 12/20/2016] [Indexed: 11/27/2022]
|
30
|
Tan YS, Reeks J, Brown CJ, Thean D, Ferrer
Gago FJ, Yuen TY, Goh EL, Lee XEC, Jennings CE, Joseph TL, Lakshminarayanan R, Lane DP, Noble MEM, Verma CS. Benzene Probes in Molecular Dynamics Simulations Reveal Novel Binding Sites for Ligand Design. J Phys Chem Lett 2016; 7:3452-7. [PMID: 27532490 PMCID: PMC5515508 DOI: 10.1021/acs.jpclett.6b01525] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Protein flexibility poses a major challenge in binding site identification. Several computational pocket detection methods that utilize small-molecule probes in molecular dynamics (MD) simulations have been developed to address this issue. Although they have proven hugely successful at reproducing experimental structural data, their ability to predict new binding sites that are yet to be identified and characterized has not been demonstrated. Here, we report the use of benzenes as probe molecules in ligand-mapping MD (LMMD) simulations to predict the existence of two novel binding sites on the surface of the oncoprotein MDM2. One of them was serendipitously confirmed by biophysical assays and X-ray crystallography to be important for the binding of a new family of hydrocarbon stapled peptides that were specifically designed to target the other putative site. These results highlight the predictive power of LMMD and suggest that predictions derived from LMMD simulations can serve as a reliable basis for the identification of novel ligand binding sites in structure-based drug design.
Collapse
Affiliation(s)
- Yaw Sing Tan
- Bioinformatics
Institute, Agency for Science, Technology
and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Judith Reeks
- Northern
Institute for Cancer Research, Newcastle
University, Framlington
Place, Newcastle upon Tyne NE2 4HH, U.K.
| | - Christopher J. Brown
- p53
Laboratory, A*STAR, 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore 138648
| | - Dawn Thean
- p53
Laboratory, A*STAR, 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore 138648
| | | | - Tsz Ying Yuen
- Institute
of Chemical & Engineering Sciences, A*STAR, 8 Biomedical
Grove, #07-01 Neuros, Singapore 138665
| | - Eunice
Tze Leng Goh
- Singapore
Eye Research Institute, 11 Third Hospital Avenue, Singapore 168751
| | - Xue Er Cheryl Lee
- p53
Laboratory, A*STAR, 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore 138648
| | - Claire E. Jennings
- Northern
Institute for Cancer Research, Newcastle
University, Framlington
Place, Newcastle upon Tyne NE2 4HH, U.K.
| | - Thomas L. Joseph
- Bioinformatics
Institute, Agency for Science, Technology
and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | | | - David P. Lane
- p53
Laboratory, A*STAR, 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore 138648
- E-mail:
| | - Martin E. M. Noble
- Northern
Institute for Cancer Research, Newcastle
University, Framlington
Place, Newcastle upon Tyne NE2 4HH, U.K.
- E-mail:
| | - Chandra S. Verma
- Bioinformatics
Institute, Agency for Science, Technology
and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
- Department
of Biological Sciences, National University
of Singapore, 14 Science
Drive 4, Singapore 117543
- School
of Biological Sciences, Nanyang Technological
University, 60 Nanyang
Drive, Singapore 637551
- E-mail:
| |
Collapse
|