1
|
Samanta R, Zhuang X, Varney KM, Weber DJ, Matysiak S. Deciphering S100B Allosteric Signaling: The Role of a Peptide Target, TRTK-12, as an Ensemble Modulator. J Chem Inf Model 2024; 64:3477-3487. [PMID: 38605537 DOI: 10.1021/acs.jcim.4c00116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
Allostery is an essential biological phenomenon in which perturbation at one site in a biomolecule elicits a functional response at a distal location(s). It is integral to biological processes, such as cellular signaling, metabolism, and transcription regulation. Understanding allostery is also crucial for rational drug discovery. In this work, we focus on an allosteric S100B protein that belongs to the S100 class of EF-hand Ca2+-binding proteins. The Ca2+-binding affinity of S100B is modulated allosterically by TRTK-12 peptide binding 25 Å away from the Ca2+-binding site. We investigated S100B allostery by carrying out nuclear magnetic resonance (NMR) measurements along with microsecond-long molecular dynamics (MD) simulations on S100B/Ca2+ with/without TRTK-12 at different NaCl salt concentrations. NMR HSQC results show that TRTK-12 reorganizes how S100B/Ca2+ responds to different salt concentrations at both orthosteric and allosteric sites. The MD data suggest that TRTK-12 breaks the dynamic aromatic and hydrogen-bond interactions (not observed in X-ray crystallographic structures) between the hinge/helix and Ca2+-binding EF-hand loop of the two subunits in the homodimeric protein. This triggers rearrangement in the protein network architectures and leads to allosteric communication. Finally, computational studies of S100B at distinct ionic strengths suggest that ligand-bound species are more robust to the changing environment relative to the S100B/Ca2+ complex.
Collapse
Affiliation(s)
- Riya Samanta
- Biophysics Graduate Program, University of Maryland, College Park, Maryland 20742, United States
| | - Xinhao Zhuang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Kristen M Varney
- Department of Biochemistry and Molecular Biology, University of Maryland, Baltimore, Maryland 20742, United States
| | - David J Weber
- IBBR, Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Silvina Matysiak
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| |
Collapse
|
2
|
Smith M, Li P. Molecular Insights into the Calcium Binding in Troponin C through a Molecular Dynamics Study. J Chem Inf Model 2023; 63:354-361. [PMID: 36507851 DOI: 10.1021/acs.jcim.2c01411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Calcium-binding proteins play critical roles in various biological processes such as signal transduction, cell growth, and transcription factor regulation. Ion binding and target binding of Ca2+-binding proteins are highly related. Therefore, understanding the ion binding mechanism will benefit the relevant inhibitor design toward the Ca2+-binding proteins. The EF-hand is the typical ion binding motif in Ca2+-binding proteins. Previous studies indicate that the ion binding affinity of the EF-hand increases with the peptide length, but this mechanism has not been fully understood. Herein, using molecular dynamics simulations, thermodynamic integration calculations, and molecular mechanics Poisson-Boltzmann surface area analysis, we systematically investigated four Ca2+-binding peptides containing the EF-hand loop in site III of rabbit skeletal troponin C. These four peptides have 13, 21, 26, and 34 residues. Our simulations reproduced the observed trend that the ion binding affinity increases with the peptide length. Our results implied that the E-helix motif preceding the EF-hand loop, likely the Phe99 residue in particular, plays a significant role in this regulation. The E-helix has a significant impact on the backbone and side-chain conformations of the Asp103 residue, rigidifying important hydrogen bonds in the EF-hand and decreasing the solvent exposure of the Ca2+ ion, hence leading to more favorable Ca2+ binding in longer peptides. The present study provides molecular insights into the ion binding in the EF-hand and establishes an important step toward elucidating the responses of Ca2+-binding proteins toward the ion and target availability.
Collapse
Affiliation(s)
- Madelyn Smith
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W. Sheridan Rd., Chicago, Illinois 60660, United States
| | - Pengfei Li
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W. Sheridan Rd., Chicago, Illinois 60660, United States
| |
Collapse
|
3
|
Wesseling CMJ, Slingerland CJ, Veraar S, Lok S, Martin NI. Structure-Activity Studies with Bis-Amidines That Potentiate Gram-Positive Specific Antibiotics against Gram-Negative Pathogens. ACS Infect Dis 2021; 7:3314-3335. [PMID: 34766746 PMCID: PMC8669655 DOI: 10.1021/acsinfecdis.1c00466] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Pentamidine, an FDA-approved
antiparasitic drug, was recently identified
as an outer membrane disrupting synergist that potentiates erythromycin,
rifampicin, and novobiocin against Gram-negative bacteria. The same
study also described a preliminary structure–activity relationship
using commercially available pentamidine analogues. We here report
the design, synthesis, and evaluation of a broader panel of bis-amidines
inspired by pentamidine. The present study both validates the previously
observed synergistic activity reported for pentamidine, while further
assessing the capacity for structurally similar bis-amidines to also
potentiate Gram-positive specific antibiotics against Gram-negative
pathogens. Among the bis-amidines prepared, a number of them were
found to exhibit synergistic activity greater than pentamidine. These
synergists were shown to effectively potentiate the activity of Gram-positive
specific antibiotics against multiple Gram-negative pathogens such
as Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas
aeruginosa, and Escherichia coli, including polymyxin- and carbapenem-resistant strains.
Collapse
Affiliation(s)
- Charlotte M. J. Wesseling
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, 2333 BE Leiden, The Netherlands
| | - Cornelis J. Slingerland
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, 2333 BE Leiden, The Netherlands
| | - Shanice Veraar
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, 2333 BE Leiden, The Netherlands
| | - Samantha Lok
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, 2333 BE Leiden, The Netherlands
| | - Nathaniel I. Martin
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, 2333 BE Leiden, The Netherlands
| |
Collapse
|
4
|
Malki Y, Martinez J, Masurier N. 1,3-Diazepine: A privileged scaffold in medicinal chemistry. Med Res Rev 2021; 41:2247-2315. [PMID: 33645848 DOI: 10.1002/med.21795] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 01/20/2021] [Accepted: 02/17/2021] [Indexed: 12/19/2022]
Abstract
Privileged structures have been widely used as effective templates for drug discovery. While benzo-1,4-diazepine constitutes the first historical example of such a structure, the 1,3 analogue is just as rich in terms of applications in medicinal chemistry. The 1,3-diazepine moiety is present in numerous biological active compounds including natural products, and is used to design compounds displaying a large range of biological activities. It is present in the clinically used anticancer compound pentostatin, in several recent FDA approved β-lactamase inhibitors (e.g., avibactam) and also in coformycin, a natural product known as a ring-expanded purine analogue displaying antiviral and anticancer activities. Several other 1,3-diazepine containing compounds have entered into clinical trials. This heterocyclic structure has been and is still widely used in medicinal chemistry to design enzyme inhibitors, GPCR ligands, and so forth. This review endeavours to highlight the main use of the 1,3-diazepine scaffold and its derivatives, and their applications in medicinal chemistry, drug design, and therapy. We will focus more particularly on the development of enzyme inhibitors incorporating this scaffold, with a strong emphasis on the molecular interactions involved in the inhibition mechanism.
Collapse
Affiliation(s)
- Yohan Malki
- IBMM, Université de Montpellier, CNRS, ENSCM, Montpellier, France
| | - Jean Martinez
- IBMM, Université de Montpellier, CNRS, ENSCM, Montpellier, France
| | - Nicolas Masurier
- IBMM, Université de Montpellier, CNRS, ENSCM, Montpellier, France
| |
Collapse
|
5
|
Kannan S, Aronica PGA, Nguyen TB, Li J, Verma CS. Computational Design of Macrocyclic Binders of S100B(ββ): Novel Peptide Theranostics. Molecules 2021; 26:721. [PMID: 33573254 PMCID: PMC7866529 DOI: 10.3390/molecules26030721] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 01/08/2023] Open
Abstract
S100B(ββ) proteins are a family of multifunctional proteins that are present in several tissues and regulate a wide variety of cellular processes. Their altered expression levels have been associated with several human diseases, such as cancer, inflammatory disorders and neurodegenerative conditions, and hence are of interest as a therapeutic target and a biomarker. Small molecule inhibitors of S100B(ββ) have achieved limited success. Guided by the wealth of available experimental structures of S100B(ββ) in complex with diverse peptides from various protein interacting partners, we combine comparative structural analysis and molecular dynamics simulations to design a series of peptides and their analogues (stapled) as S100B(ββ) binders. The stapled peptides were subject to in silico mutagenesis experiments, resulting in optimized analogues that are predicted to bind to S100B(ββ) with high affinity, and were also modified with imaging agents to serve as diagnostic tools. These stapled peptides can serve as theranostics, which can be used to not only diagnose the levels of S100B(ββ) but also to disrupt the interactions of S100B(ββ) with partner proteins which drive disease progression, thus serving as novel therapeutics.
Collapse
Affiliation(s)
- Srinivasaraghavan Kannan
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore; (P.G.A.A.); (T.B.N.); (J.L.)
| | - Pietro G. A. Aronica
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore; (P.G.A.A.); (T.B.N.); (J.L.)
| | - Thanh Binh Nguyen
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore; (P.G.A.A.); (T.B.N.); (J.L.)
| | - Jianguo Li
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore; (P.G.A.A.); (T.B.N.); (J.L.)
- Singapore Eye Research Institute, Singapore 169856, Singapore
| | - Chandra S. Verma
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore; (P.G.A.A.); (T.B.N.); (J.L.)
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| |
Collapse
|
6
|
Young BD, Yu W, Rodríguez DJV, Varney KM, MacKerell AD, Weber DJ. Specificity of Molecular Fragments Binding to S100B versus S100A1 as Identified by NMR and Site Identification by Ligand Competitive Saturation (SILCS). Molecules 2021; 26:E381. [PMID: 33450915 PMCID: PMC7828390 DOI: 10.3390/molecules26020381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/08/2021] [Accepted: 01/09/2021] [Indexed: 12/29/2022] Open
Abstract
S100B, a biomarker of malignant melanoma, interacts with the p53 protein and diminishes its tumor suppressor function, which makes this S100 family member a promising therapeutic target for treating malignant melanoma. However, it is a challenge to design inhibitors that are specific for S100B in melanoma versus other S100-family members that are important for normal cellular activities. For example, S100A1 is most similar in sequence and structure to S100B, and this S100 protein is important for normal skeletal and cardiac muscle function. Therefore, a combination of NMR and computer aided drug design (CADD) was used to initiate the design of specific S100B inhibitors. Fragment-based screening by NMR, also termed "SAR by NMR," is a well-established method, and was used to examine spectral perturbations in 2D [1H, 15N]-HSQC spectra of Ca2+-bound S100B and Ca2+-bound S100A1, side-by-side, and under identical conditions for comparison. Of the 1000 compounds screened, two were found to be specific for binding Ca2+-bound S100A1 and four were found to be specific for Ca2+-bound S100B, respectively. The NMR spectral perturbations observed in these six data sets were then used to model how each of these small molecule fragments showed specificity for one S100 versus the other using a CADD approach termed Site Identification by Ligand Competitive Saturation (SILCS). In summary, the combination of NMR and computational approaches provided insight into how S100A1 versus S100B bind small molecules specifically, which will enable improved drug design efforts to inhibit elevated S100B in melanoma. Such a fragment-based approach can be used generally to initiate the design of specific inhibitors for other highly homologous drug targets.
Collapse
Affiliation(s)
- Brianna D. Young
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene St., Baltimore, MD 21201, USA; (B.D.Y.); (D.J.V.R.); (K.M.V.)
- Center for Biomolecular Therapeutics (CBT), Baltimore, MD 21201, USA; (W.Y.); (A.D.M.J.)
| | - Wenbo Yu
- Center for Biomolecular Therapeutics (CBT), Baltimore, MD 21201, USA; (W.Y.); (A.D.M.J.)
- Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
- Institute for Bioscience and Biotechnology Research (IBBR), Rockville, MD 20850, USA
| | - Darex J. Vera Rodríguez
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene St., Baltimore, MD 21201, USA; (B.D.Y.); (D.J.V.R.); (K.M.V.)
- Center for Biomolecular Therapeutics (CBT), Baltimore, MD 21201, USA; (W.Y.); (A.D.M.J.)
| | - Kristen M. Varney
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene St., Baltimore, MD 21201, USA; (B.D.Y.); (D.J.V.R.); (K.M.V.)
- Center for Biomolecular Therapeutics (CBT), Baltimore, MD 21201, USA; (W.Y.); (A.D.M.J.)
- Institute for Bioscience and Biotechnology Research (IBBR), Rockville, MD 20850, USA
| | - Alexander D. MacKerell
- Center for Biomolecular Therapeutics (CBT), Baltimore, MD 21201, USA; (W.Y.); (A.D.M.J.)
- Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
- Institute for Bioscience and Biotechnology Research (IBBR), Rockville, MD 20850, USA
| | - David J. Weber
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene St., Baltimore, MD 21201, USA; (B.D.Y.); (D.J.V.R.); (K.M.V.)
- Center for Biomolecular Therapeutics (CBT), Baltimore, MD 21201, USA; (W.Y.); (A.D.M.J.)
- Institute for Bioscience and Biotechnology Research (IBBR), Rockville, MD 20850, USA
| |
Collapse
|
7
|
Wu KJ, Wang W, Wang HMD, Leung CH, Ma DL. Interfering with S100B-effector protein interactions for cancer therapy. Drug Discov Today 2020; 25:1754-1761. [PMID: 32679172 DOI: 10.1016/j.drudis.2020.07.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 06/17/2020] [Accepted: 07/02/2020] [Indexed: 12/17/2022]
Abstract
S100 calcium-binding protein B (S100B) is overexpressed in various malignant tumors, where it regulates cancer cell proliferation and metabolism by physical interactions with other molecules. Interfering with S100B-effector protein interactions is a potential strategy to treat malignant tumors. Although some S100B inhibitors have been discovered by virtual screening (VS), most target the S100B-p53 interaction. Hence, there is scope for the discovery of other S100B-effector protein interaction modulators for malignant tumors. In this review, we provide an overview of S100B-effector protein interaction inhibitor discovery using VS and discuss promising S100B-effector protein interaction targets that permit in silico analysis for drug discovery.
Collapse
Affiliation(s)
- Ke-Jia Wu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa 999078, Macao SAR, China
| | - Wanhe Wang
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong 999077, Hong Kong, China
| | - Hui-Min David Wang
- Graduate Institute of Biomedical Engineering, National Chung Hsing University, Taichung 402, Taiwan
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa 999078, Macao SAR, China.
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong 999077, Hong Kong, China.
| |
Collapse
|
8
|
Baudier J, Deloulme JC, Shaw GS. The Zn 2+ and Ca 2+ -binding S100B and S100A1 proteins: beyond the myths. Biol Rev Camb Philos Soc 2020; 95:738-758. [PMID: 32027773 DOI: 10.1111/brv.12585] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 01/06/2020] [Accepted: 01/20/2020] [Indexed: 12/17/2022]
Abstract
The S100 genes encode a conserved group of 21 vertebrate-specific EF-hand calcium-binding proteins. Since their discovery in 1965, S100 proteins have remained enigmatic in terms of their cellular functions. In this review, we summarize the calcium- and zinc-binding properties of the dimeric S100B and S100A1 proteins and highlight data that shed new light on the extracellular and intracellular regulation and functions of S100B. We point out that S100B and S100A1 homodimers are not functionally interchangeable and that in a S100A1/S100B heterodimer, S100A1 acts as a negative regulator for the ability of S100B to bind Zn2+ . The Ca2+ and Zn2+ -dependent interactions of S100B with a wide array of proteins form the basis of its activities and have led to the derivation of some initial rules for S100B recognition of protein targets. However, recent findings have strongly suggested that these rules need to be revisited. Here, we describe a new consensus S100B binding motif present in intracellular and extracellular vertebrate-specific proteins and propose a new model for stable interactions of S100B dimers with full-length target proteins. A chaperone-associated function for intracellular S100B in adaptive cellular stress responses is also discussed. This review may help guide future studies on the functions of S100 proteins in general.
Collapse
Affiliation(s)
- Jacques Baudier
- Institut de Biologie du Développement de Marseille-UMR CNRS 7288, Aix Marseille Université, 13288, Marseille Cedex 9, France
| | - Jean Christophe Deloulme
- Grenoble Institut des Neurosciences, INSERM U1216, Université Grenoble Alpes, 38000, Grenoble, France
| | - Gary S Shaw
- Department of Biochemistry, University of Western Ontario, London, Ontario, N6A5C1, Canada
| |
Collapse
|
9
|
Amaral PDA, Autheman D, de Melo GD, Gouault N, Cupif JF, Goyard S, Dutra P, Coatnoan N, Cosson A, Monet D, Saul F, Haouz A, Uriac P, Blondel A, Minoprio P. Designed mono- and di-covalent inhibitors trap modeled functional motions for Trypanosoma cruzi proline racemase in crystallography. PLoS Negl Trop Dis 2018; 12:e0006853. [PMID: 30372428 PMCID: PMC6224121 DOI: 10.1371/journal.pntd.0006853] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 11/08/2018] [Accepted: 09/18/2018] [Indexed: 11/19/2022] Open
Abstract
Chagas disease, caused by Trypanosoma cruzi, affects millions of people in South America and no satisfactory therapy exists, especially for its life threatening chronic phase. We targeted the Proline Racemase of T. cruzi, which is present in all stages of the parasite life cycle, to discover new inhibitors against this disease. The first published crystal structures of the enzyme revealed that the catalytic site is too small to allow any relevant drug design. In previous work, to break through the chemical space afforded to virtual screening and drug design, we generated intermediate models between the open (ligand free) and closed (ligand bound) forms of the enzyme. In the present work, we co-crystallized the enzyme with the selected inhibitors and found that they were covalently bound to the catalytic cysteine residues in the active site, thus explaining why these compounds act as irreversible inhibitors. These results led us to the design of a novel, more potent specific inhibitor, NG-P27. Co-crystallization of this new inhibitor with the enzyme allowed us to confirm the predicted protein functional motions and further characterize the chemical mechanism. Hence, the catalytic Cys300 sulfur atom of the enzyme attacks the C2 carbon of the inhibitor in a coupled, regiospecific—stereospecific Michael reaction with trans-addition of a proton on the C3 carbon. Strikingly, the six different conformations of the catalytic site in the crystal structures reported in this work had key similarities to our intermediate models previously generated by inference of the protein functional motions. These crystal structures span a conformational interval covering roughly the first quarter of the opening mechanism, demonstrating the relevance of modeling approaches to break through chemical space in drug design. There is an urgent need to develop innovative medicines addressing neglected diseases, multi-drug resistance and other unmet therapeutic needs. To create new drug design opportunities, we attempted to exploit protein functional motions by using a rational approach to model structural intermediates of a therapeutic target. After successfully designing inhibitors based on modeled intermediates of T. Cruzi proline racemase, the determination of crystal structures of the target protein in complex with the inhibitors revealed conformations that were strikingly close to the predicted models. Thus, beyond the discovery of compounds establishing a novel mode of action that can lead to innovative treatments of Chagas disease, we illustrate how modeling protein functional motions can be exploited in a rational approach to create opportunities in drug design.
Collapse
Affiliation(s)
- Patricia de Aguiar Amaral
- Université de Rennes 1, Equipe Chimie organique et interfaces (CORINT), UMR 6226 Sciences Chimiques de Rennes, Rennes, France
| | - Delphine Autheman
- Institut Pasteur, Laboratoire des Processus Infectieux à Trypanosomatidés, Département Infection et Epidémiologie, Paris, France
| | - Guilherme Dias de Melo
- Institut Pasteur, Laboratoire des Processus Infectieux à Trypanosomatidés, Département Infection et Epidémiologie, Paris, France
| | - Nicolas Gouault
- Université de Rennes 1, Equipe Chimie organique et interfaces (CORINT), UMR 6226 Sciences Chimiques de Rennes, Rennes, France
| | - Jean-François Cupif
- Université de Rennes 1, Equipe Chimie organique et interfaces (CORINT), UMR 6226 Sciences Chimiques de Rennes, Rennes, France
| | - Sophie Goyard
- Institut Pasteur, Laboratoire des Processus Infectieux à Trypanosomatidés, Département Infection et Epidémiologie, Paris, France
| | - Patricia Dutra
- Institut Pasteur, Laboratoire des Processus Infectieux à Trypanosomatidés, Département Infection et Epidémiologie, Paris, France
| | - Nicolas Coatnoan
- Institut Pasteur, Laboratoire des Processus Infectieux à Trypanosomatidés, Département Infection et Epidémiologie, Paris, France
| | - Alain Cosson
- Institut Pasteur, Laboratoire des Processus Infectieux à Trypanosomatidés, Département Infection et Epidémiologie, Paris, France
| | - Damien Monet
- Institut Pasteur, Unité de Bioinformatique Structurale, Département de Biologie Structurale et Chimie, CNRS-UMR 3528, Paris, France
| | - Frederick Saul
- Institut Pasteur, Plateforme de Cristallographie, Département de Biologie Structurale et Chimie, CNRS-UMR 3528, Paris, France
| | - Ahmed Haouz
- Institut Pasteur, Plateforme de Cristallographie, Département de Biologie Structurale et Chimie, CNRS-UMR 3528, Paris, France
| | - Philippe Uriac
- Université de Rennes 1, Equipe Chimie organique et interfaces (CORINT), UMR 6226 Sciences Chimiques de Rennes, Rennes, France
- * E-mail: (PU); (AB); (PM)
| | - Arnaud Blondel
- Institut Pasteur, Unité de Bioinformatique Structurale, Département de Biologie Structurale et Chimie, CNRS-UMR 3528, Paris, France
- * E-mail: (PU); (AB); (PM)
| | - Paola Minoprio
- Institut Pasteur, Laboratoire des Processus Infectieux à Trypanosomatidés, Département Infection et Epidémiologie, Paris, France
- * E-mail: (PU); (AB); (PM)
| |
Collapse
|
10
|
Abstract
The S100B protein is an intra- and extracellular signaling protein that
plays a role in a multitude of cellular processes and abnormal S100B is
associated with various neurological diseases and cancers. S100B recognizes and
binds effector proteins in a calcium-dependent manner. S100B has been shown to
interact with the actin capping protein CapZ, protein kinase C, Hdm2 and 4, RAGE
receptor, and p53, among others. These protein partners interact with
a common area on the S100B protein surface, validating the method of using the
consensus sequence for S100B target search. In addition, each S100B target
protein distinguishes itself by additional contacts with S100B. This perspective
suggests that the combination of sequence homology search and structural
analysis promises to identify newer S100B-binding partners beyond the use of the
consensus sequence alone as the given example in the XPB subunit of the TFIIH
general transcription factor. XPB is a helicase required for both transcription
and DNA repair. Inherited xpb mutations are associated with human disease
Xeroderma Pigmentasum, Cockayne syndrome, and trichothiodystrophy. S100B protein
is likely associated with much more biological pathways and processes. We
believe that S100B will attract more and more attentions in the scientific
community and S100B related studies will have important implications in human
health and medicine.
Collapse
Affiliation(s)
- K D Prez
- Department of Biochemistry, University of California Riverside, 900 University Ave, Riverside, California, USA
| | - L Fan
- Department of Biochemistry, University of California Riverside, 900 University Ave, Riverside, California, USA
| |
Collapse
|
11
|
Melville Z, Aligholizadeh E, McKnight LE, Weber DJ, Pozharski E, Weber DJ. X-ray crystal structure of human calcium-bound S100A1. Acta Crystallogr F Struct Biol Commun 2017; 73:215-221. [PMID: 28368280 PMCID: PMC5379171 DOI: 10.1107/s2053230x17003983] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 03/11/2017] [Indexed: 01/02/2023] Open
Abstract
S100A1 is a member of the S100 family of Ca2+-binding proteins and regulates several cellular processes, including those involved in Ca2+ signaling and cardiac and skeletal muscle function. In Alzheimer's disease, brain S100A1 is overexpressed and gives rise to disease pathologies, making it a potential therapeutic target. The 2.25 Å resolution crystal structure of Ca2+-S100A1 is solved here and is compared with the structures of other S100 proteins, most notably S100B, which is a highly homologous S100-family member that is implicated in the progression of malignant melanoma. The observed structural differences in S100A1 versus S100B provide insights regarding target protein-binding specificity and for targeting these two S100 proteins in human diseases using structure-based drug-design approaches.
Collapse
Affiliation(s)
- Zephan Melville
- Center for Biomolecular Therapeutics, Department of Biochemistry and Molecular Biology, University of Maryland Baltimore, 108 North Greene Street, Baltimore, MD 21201, USA
| | - Ehson Aligholizadeh
- Center for Biomolecular Therapeutics, Department of Biochemistry and Molecular Biology, University of Maryland Baltimore, 108 North Greene Street, Baltimore, MD 21201, USA
| | - Laura E. McKnight
- Center for Biomolecular Therapeutics, Department of Biochemistry and Molecular Biology, University of Maryland Baltimore, 108 North Greene Street, Baltimore, MD 21201, USA
| | - Dylan J. Weber
- Center for Biomolecular Therapeutics, Department of Biochemistry and Molecular Biology, University of Maryland Baltimore, 108 North Greene Street, Baltimore, MD 21201, USA
| | - Edwin Pozharski
- Center for Biomolecular Therapeutics, Department of Biochemistry and Molecular Biology, University of Maryland Baltimore, 108 North Greene Street, Baltimore, MD 21201, USA
| | - David J. Weber
- Center for Biomolecular Therapeutics, Department of Biochemistry and Molecular Biology, University of Maryland Baltimore, 108 North Greene Street, Baltimore, MD 21201, USA
- Marlene and Stewart Greenebaum Cancer Center, University of Maryland Baltimore, 108 North Greene Street, Baltimore, MD 21201, USA
| |
Collapse
|
12
|
Guvench O. Computational functional group mapping for drug discovery. Drug Discov Today 2016; 21:1928-1931. [PMID: 27393487 DOI: 10.1016/j.drudis.2016.06.030] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 06/23/2016] [Accepted: 06/29/2016] [Indexed: 01/05/2023]
Abstract
Computational functional group mapping (cFGM) is emerging as a high-impact complement to existing widely used experimental and computational structure-based drug discovery methods. cFGM provides comprehensive atomic-resolution 3D maps of the affinity of functional groups that can constitute drug-like molecules for a given target, typically a protein. These 3D maps can be intuitively and interactively visualized by medicinal chemists to rapidly design synthetically accessible ligands. Given that the maps can inform selection of functional groups for affinity, specificity, and pharmacokinetic properties, they are of utility for both the optimization of existing drug candidates and creating novel ones. Here, I review recent advances in cFGM with emphasis on the unique information content in the approach that offers the potential of broadly facilitating structure-based ligand design.
Collapse
Affiliation(s)
- Olgun Guvench
- SilcsBio, LLC, 8 Market Street, Suite 300, Baltimore, MD 21202, USA.
| |
Collapse
|
13
|
Cavalier MC, Melville Z, Aligholizadeh E, Raman EP, Yu W, Fang L, Alasady M, Pierce AD, Wilder PT, MacKerell AD, Weber DJ. Novel protein-inhibitor interactions in site 3 of Ca(2+)-bound S100B as discovered by X-ray crystallography. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:753-60. [PMID: 27303795 DOI: 10.1107/s2059798316005532] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/02/2016] [Indexed: 02/07/2023]
Abstract
Structure-based drug discovery is under way to identify and develop small-molecule S100B inhibitors (SBiXs). Such inhibitors have therapeutic potential for treating malignant melanoma, since high levels of S100B downregulate wild-type p53 tumor suppressor function in this cancer. Computational and X-ray crystallographic studies of two S100B-SBiX complexes are described, and both compounds (apomorphine hydrochloride and ethidium bromide) occupy an area of the S100B hydrophobic cleft which is termed site 3. These data also reveal novel protein-inhibitor interactions which can be used in future drug-design studies to improve SBiX affinity and specificity. Of particular interest, apomorphine hydrochloride showed S100B-dependent killing in melanoma cell assays, although the efficacy exceeds its affinity for S100B and implicates possible off-target contributions. Because there are no structural data available for compounds occupying site 3 alone, these studies contribute towards the structure-based approach to targeting S100B by including interactions with residues in site 3 of S100B.
Collapse
Affiliation(s)
- Michael C Cavalier
- Department of Biochemistry and Molecular Biology, Center for Biomolecular Therapeutics (CBT), University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Zephan Melville
- Department of Biochemistry and Molecular Biology, Center for Biomolecular Therapeutics (CBT), University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Ehson Aligholizadeh
- Department of Biochemistry and Molecular Biology, Center for Biomolecular Therapeutics (CBT), University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - E Prabhu Raman
- Computer Aided Drug Design Center, University of Maryland School of Pharmacy, Baltimore, MD 21201, USA
| | - Wenbo Yu
- Computer Aided Drug Design Center, University of Maryland School of Pharmacy, Baltimore, MD 21201, USA
| | - Lei Fang
- Computer Aided Drug Design Center, University of Maryland School of Pharmacy, Baltimore, MD 21201, USA
| | - Milad Alasady
- Department of Biochemistry and Molecular Biology, Center for Biomolecular Therapeutics (CBT), University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Adam D Pierce
- Department of Biochemistry and Molecular Biology, Center for Biomolecular Therapeutics (CBT), University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Paul T Wilder
- Department of Biochemistry and Molecular Biology, Center for Biomolecular Therapeutics (CBT), University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Alexander D MacKerell
- Computer Aided Drug Design Center, University of Maryland School of Pharmacy, Baltimore, MD 21201, USA
| | - David J Weber
- Department of Biochemistry and Molecular Biology, Center for Biomolecular Therapeutics (CBT), University of Maryland School of Medicine, Baltimore, MD 21201, USA
| |
Collapse
|