101
|
Molecular basis of the beta-lactamase protein using comparative modelling, drug screening and molecular dynamics studies to understand the resistance of β-lactam antibiotics. J Mol Model 2020; 26:200. [PMID: 32638150 DOI: 10.1007/s00894-020-04459-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 06/28/2020] [Indexed: 02/06/2023]
Abstract
Beta-lactamase (ampC) in general causes the onset of antibiotic resistance in pathogenic bacteria against the β-lactam antibiotics. Morganella morganii which belongs to the Proteae tribe of the Enterobacteriaceae family is a Gram-negative bacillus. Gram-negative bacteria are the key problematic agents among the human population in overexpressing resistance against β-lactam antibiotics. These β-lactam antibiotics being experimentally well studied still lack the key information and mechanism for their resistance. The structural information of the ampC protein is unknown and poorly studied; hence, it is the need of the hour to find effective inhibitors against it. In our study, the prediction of the three-dimensional structure of ampC protein from Morganella morganii was performed using a comparative modelling approach. The predicted structure was energetically stabilized and functional conformations were mapped through 100-ns molecular dynamics simulation runs. Also, Ramachandran plot shows the model to be stereo-chemically stable with most residues found under core allowed regions. Drug screening with several experimentally tested inhibitors was then confirmed to check the activity against ampC protein using an AutoDock tool. The results suggested OncoglabrinolC molecule as the best inhibitor (out of 21 drug molecules) with a binding affinity of - 11.44 kcal/mol. Anti-bacterial/anti-parasitic inhibitors have not only been used against bacterial infections, but later reports have also shown them to work against deadly viruses such as SARS-CoV2. This key structural and inhibitory information is certain to help in the discovery of specific and potent substitute therapeutic drugs and the development of experimental procedures against human infection.
Collapse
|
102
|
Jukič M, Konc J, Janežič D, Bren U. ProBiS H2O MD Approach for Identification of Conserved Water Sites in Protein Structures for Drug Design. ACS Med Chem Lett 2020; 11:877-882. [PMID: 32435399 PMCID: PMC7236268 DOI: 10.1021/acsmedchemlett.9b00651] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 03/19/2020] [Indexed: 01/06/2023] Open
Abstract
![]()
The ProBiS H2O MD
approach for identification of conserved waters
and water sites of interest in macromolecular systems, which is becoming
a typical step in a structure-based drug design or macromolecular
study in general, is described. This work explores an extension of
the ProBiS H2O approach introduced by Jukič et al. Indeed,
water molecules are key players in the interaction mechanisms of macromolecules
and small molecules and play structural roles. Our earlier developed
approach, ProBiS H2O, is a simple and transparent workflow for conserved
water detection. Here we have considered generalizing the idea by
supplementing the experimental data with data derived from molecular
dynamics to facilitate work on less known systems. Newly developed
ProBiS H2O MD workflow uses trajectory data, extracts and identifies
interesting water sites, and visualizes the results. ProBiS H2O MD
can thus robustly process molecular dynamic trajectory snapshots,
perform local superpositions, collect water location data, and perform
density-based clustering to identify discrete sites with high conservation
of water molecules. This is a new approach that uses experimental
data in silico to identify interesting water sites.
Methodology is fast and water-model or molecular dynamics software
independent. Trends in the conservation of water molecules can be
followed over a variety of trajectories, and our approach has been
successfully validated using reported protein systems with experimentally
observed conserved water molecules. ProBiS H2O MD is freely available
as PyMOL plugin at http://insilab.org.
Collapse
Affiliation(s)
- Marko Jukič
- University of Maribor, Faculty of Chemistry and Chemical Engineering, Laboratory of Physical Chemistry and Chemical Thermodynamics, Smetanova ulica 17, SI-2000 Maribor, Slovenia
- University of Primorska, Faculty of Mathematics, Natural Sciences and Information Technologies, Glagoljaška 8, SI-6000 Koper, Slovenia
| | - Janez Konc
- University of Maribor, Faculty of Chemistry and Chemical Engineering, Laboratory of Physical Chemistry and Chemical Thermodynamics, Smetanova ulica 17, SI-2000 Maribor, Slovenia
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Dušanka Janežič
- University of Primorska, Faculty of Mathematics, Natural Sciences and Information Technologies, Glagoljaška 8, SI-6000 Koper, Slovenia
| | - Urban Bren
- University of Maribor, Faculty of Chemistry and Chemical Engineering, Laboratory of Physical Chemistry and Chemical Thermodynamics, Smetanova ulica 17, SI-2000 Maribor, Slovenia
- University of Primorska, Faculty of Mathematics, Natural Sciences and Information Technologies, Glagoljaška 8, SI-6000 Koper, Slovenia
| |
Collapse
|
103
|
Gentile D, Patamia V, Scala A, Sciortino MT, Piperno A, Rescifina A. Putative Inhibitors of SARS-CoV-2 Main Protease from A Library of Marine Natural Products: A Virtual Screening and Molecular Modeling Study. Mar Drugs 2020; 18:E225. [PMID: 32340389 PMCID: PMC7231030 DOI: 10.3390/md18040225] [Citation(s) in RCA: 204] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/10/2020] [Accepted: 04/20/2020] [Indexed: 12/14/2022] Open
Abstract
The current emergency due to the worldwide spread of the COVID-19 caused by the new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a great concern for global public health. Already in the past, the outbreak of severe acute respiratory syndrome (SARS) in 2003 and Middle Eastern respiratory syndrome (MERS) in 2012 demonstrates the potential of coronaviruses to cross-species borders and further underlines the importance of identifying new-targeted drugs. An ideal antiviral agent should target essential proteins involved in the lifecycle of SARS-CoV. Currently, some HIV protease inhibitors (i.e., Lopinavir) are proposed for the treatment of COVID-19, although their effectiveness has not yet been assessed. The main protease (Mpr) provides a highly validated pharmacological target for the discovery and design of inhibitors. We identified potent Mpr inhibitors employing computational techniques that entail the screening of a Marine Natural Product (MNP) library. MNP library was screened by a hyphenated pharmacophore model, and molecular docking approaches. Molecular dynamics and re-docking further confirmed the results obtained by structure-based techniques and allowed this study to highlight some crucial aspects. Seventeen potential SARS-CoV-2 Mpr inhibitors have been identified among the natural substances of marine origin. As these compounds were extensively validated by a consensus approach and by molecular dynamics, the likelihood that at least one of these compounds could be bioactive is excellent.
Collapse
Affiliation(s)
- Davide Gentile
- Department of Drug Sciences, University of Catania, V.le A. Doria, 95125 Catania, Italy;
| | - Vincenzo Patamia
- Department of Drug Sciences, University of Catania, V.le A. Doria, 95125 Catania, Italy;
| | - Angela Scala
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, V.le F. Stagno d’Alcontres 31, 98166 Messina, Italy; (A.S.); (M.T.S.); (A.P.)
| | - Maria Teresa Sciortino
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, V.le F. Stagno d’Alcontres 31, 98166 Messina, Italy; (A.S.); (M.T.S.); (A.P.)
| | - Anna Piperno
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, V.le F. Stagno d’Alcontres 31, 98166 Messina, Italy; (A.S.); (M.T.S.); (A.P.)
| | - Antonio Rescifina
- Department of Drug Sciences, University of Catania, V.le A. Doria, 95125 Catania, Italy;
- Consorzio Interuniversitario Nazionale di ricerca in Metodologie e Processi Innovativi di Sintesi (CINMPS), Via E. Orabona, 4, 70125 Bari, Italy
| |
Collapse
|
104
|
Odhar HA, Ahjel SW, Albeer AAA, Hashim AF, Rayshan AM, Humadi SS. Molecular docking and dynamics simulation of FDA approved drugs with the main protease from 2019 novel coronavirus. Bioinformation 2020; 16:236-244. [PMID: 32308266 PMCID: PMC7147498 DOI: 10.6026/97320630016236] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/10/2020] [Accepted: 03/20/2020] [Indexed: 12/20/2022] Open
Abstract
Design and development of an effective drug to combat the 2019 novel coronavirus remains a challenge. Therefore, it is of interest to study the binding features of 1615 FDA approved drugs with the recently known 2019-nCoV main protease structure having high sequence homology with that from SARS-CoV. We document the binding features of top 10 drugs with the target protein. We further report that Conivaptan and Azelastine are mainly involved in hydrophobic interactions with active site residues. Both drugs can maintain close proximity to the binding pocket of main protease during simulation. However, these data need further in vitro and in vivo evaluation to repurpose these two drugs against 2019-nCoV.
Collapse
Affiliation(s)
| | | | | | | | | | - Suhad Sami Humadi
- Department of pharmacy, Al-Zahrawi University College, Karbala, Iraq
| |
Collapse
|
105
|
Hup-Type Hydrogenases of Purple Bacteria: Homology Modeling and Computational Assessment of Biotechnological Potential. Int J Mol Sci 2020; 21:ijms21010366. [PMID: 31935912 PMCID: PMC6981441 DOI: 10.3390/ijms21010366] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/26/2019] [Accepted: 01/01/2020] [Indexed: 01/01/2023] Open
Abstract
Three-dimensional structures of six closely related hydrogenases from purple bacteria were modeled by combining the template-based and ab initio modeling approach. The results led to the conclusion that there should be a 4Fe3S cluster in the structure of these enzymes. Thus, these hydrogenases could draw interest for exploring their oxygen tolerance and practical applicability in hydrogen fuel cells. Analysis of the 4Fe3S cluster’s microenvironment showed intragroup heterogeneity. A possible function of the C-terminal part of the small subunit in membrane binding is discussed. Comparison of the built models with existing hydrogenases of the same subgroup (membrane-bound oxygen-tolerant hydrogenases) was carried out. Analysis of intramolecular interactions in the large subunits showed statistically reliable differences in the number of hydrophobic interactions and ionic interactions. Molecular tunnels were mapped in the models and compared with structures from the PDB. Protein–protein docking showed that these enzymes could exchange electrons in an oligomeric state, which is important for oxygen-tolerant hydrogenases. Molecular docking with model electrode compounds showed mostly the same results as with hydrogenases from E. coli, H. marinus, R. eutropha, and S. enterica; some interesting results were shown in case of HupSL from Rba. sphaeroides and Rvi. gelatinosus.
Collapse
|
106
|
Dash R, Ali MC, Dash N, Azad MAK, Hosen SMZ, Hannan MA, Moon IS. Structural and Dynamic Characterizations Highlight the Deleterious Role of SULT1A1 R213H Polymorphism in Substrate Binding. Int J Mol Sci 2019; 20:ijms20246256. [PMID: 31835852 PMCID: PMC6969939 DOI: 10.3390/ijms20246256] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/04/2019] [Accepted: 12/09/2019] [Indexed: 12/16/2022] Open
Abstract
Sulfotransferase 1A1 (SULT1A1) is responsible for catalyzing various types of endogenous and exogenous compounds. Accumulating data indicates that the polymorphism rs9282861 (R213H) is responsible for inefficient enzymatic activity and associated with cancer progression. To characterize the detailed functional consequences of this mutation behind the loss-of-function of SULT1A1, the present study deployed molecular dynamics simulation to get insights into changes in the conformation and binding energy. The dynamics scenario of SULT1A1 in both wild and mutated types as well as with and without ligand showed that R213H induced local conformational changes, especially in the substrate-binding loop rather than impairing overall stability of the protein structure. The higher conformational changes were observed in the loop3 (residues, 235-263), turning loop conformation to A-helix and B-bridge, which ultimately disrupted the plasticity of the active site. This alteration reduced the binding site volume and hydrophobicity to decrease the binding affinity of the enzyme to substrates, which was highlighted by the MM-PBSA binding energy analysis. These findings highlight the key insights of structural consequences caused by R213H mutation, which would enrich the understanding regarding the role of SULT1A1 mutation in cancer development and also xenobiotics management to individuals in the different treatment stages.
Collapse
Affiliation(s)
- Raju Dash
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Korea
| | - Md Chayan Ali
- Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia 7003, Bangladesh
| | - Nayan Dash
- Department of Computer Science and Engineering, BGC Trust University, Bangladesh, Chittagong 4381, Bangladesh
| | - Md Abul Kalam Azad
- Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia 7003, Bangladesh
| | - S M Zahid Hosen
- Pancreatic Research Group, South Western Sydney Clinical School, University of New South Wales, and Ingham Institute for Applied Medical Research, Liverpool, NSW 2170, Australia
| | - Md Abdul Hannan
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Korea
- Department of Biochemistry and Molecular Biology, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Il Soo Moon
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Korea
| |
Collapse
|
107
|
Floresta G, Patamia V, Gentile D, Molteni F, Santamato A, Rescifina A, Vecchio M. Repurposing of FDA-Approved Drugs for Treating Iatrogenic Botulism: A Paired 3D-QSAR/Docking Approach †. ChemMedChem 2019; 15:256-262. [PMID: 31774239 DOI: 10.1002/cmdc.201900594] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/24/2019] [Indexed: 12/17/2022]
Abstract
Botulinum neurotoxin (BoNT) is widely used for the treatment of spasticity, focal dystonia, chronic migraine, facial hemispasm, and facial aesthetic treatments. Generally, treatment with botulinum toxin is a safe procedure when conducted by clinicians with expertise, and local side effects are rare and transient. However, occasionally adverse effects can occur due to the spread of the drug to nontargeted muscles and organs, producing dry mouth, fatigue, and flu-like symptoms, up to signs of systemic botulism, which appears to be more frequent in children treated for spasticity than in adults. In silico 3D-QSAR and molecular docking studies were performed to build a structure-based model on selected potent known botulinum neurotoxin type A inhibitors; this was used to screen the US Food and Drug Administration (FDA) database. Thirty molecules were identified as possible light-chain BoNT/A inhibitors. In this study, we applied a well-established ligand- and structure-based methodology for the identification of hit compounds among a database of FDA-approved drugs. The identification of budesonide, protirelin, and ciclesonide followed by other compounds can be considered a starting point for investigations of selected compounds that could bypass much of the time and costs involved in the drug approval process.
Collapse
Affiliation(s)
- Giuseppe Floresta
- Department of Drug Sciences, University of Catania, V.le A. Doria, 95125, Catania, Italy
| | - Vincenzo Patamia
- Department of Drug Sciences, University of Catania, V.le A. Doria, 95125, Catania, Italy
| | - Davide Gentile
- Department of Drug Sciences, University of Catania, V.le A. Doria, 95125, Catania, Italy
| | - Franco Molteni
- Villa Beretta Rehabilitation Center, Valduce Hospital, 23845, Costa Masnaga, Lecco, Italy
| | - Andrea Santamato
- Spasticity and Movement Disorders "ReSTaRt" Unit, Physical Medicine and Rehabilitation Section, OORR Hospital, University of Foggia, 71122, Foggia, Italy
| | - Antonio Rescifina
- Department of Drug Sciences, University of Catania, V.le A. Doria, 95125, Catania, Italy.,Consorzio Interuniversitario Nazionale di ricerca in Metodologie e Processi Innovativi di Sintesi (C.I.N.M.P.S.), Via E. Orabona, 4, 70125, Bari, Italy
| | - Michele Vecchio
- Department of Biomedical and Biotechnological Sciences, Section of Pharmacology, University of Catania, Via S. Sofia 67, 95123, Catania, Italy
| |
Collapse
|
108
|
Biolubrication synergy: Hyaluronan - Phospholipid interactions at interfaces. Adv Colloid Interface Sci 2019; 274:102050. [PMID: 31669714 DOI: 10.1016/j.cis.2019.102050] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 10/15/2019] [Accepted: 10/16/2019] [Indexed: 11/24/2022]
Abstract
The manner in which nature has solved lubrication issues has fascinated scientists for centuries, in particular when considering that lubrication is achieved in aqueous media. The most outstanding system in this respect is likely the synovial joint, where close to frictionless motion is realized under different loads and shear rates. This review article focuses on two components present in the synovial area, hyaluronan and phospholipids. We recapitulate what has been learned about their interactions at interfaces from recent experiments, with focus on results obtained using reflectivity techniques at large scale facilities. In parallel, modelling experiments have been carried out and from these efforts new detailed knowledge about how hyaluronan and phospholipids interact has been gained. In this review we combine findings from modelling and experiments to gain deeper insight. Finally, we summarize what has been learned of the lubrication performance of mixtures of phospholipids and hyaluronan.
Collapse
|
109
|
Cruz-Torres I, Backos DS, Herson PS. Characterization and Optimization of the Novel Transient Receptor Potential Melastatin 2 Antagonist tatM2NX. Mol Pharmacol 2019; 97:102-111. [PMID: 31772034 DOI: 10.1124/mol.119.117549] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 11/18/2019] [Indexed: 12/12/2022] Open
Abstract
Transient receptor potential melastatin 2 (TRPM2) is a calcium-permeable channel activated by adenosine diphosphate ribose metabolites and oxidative stress. TRPM2 contributes to neuronal injury in the brain caused by stroke and cardiac arrest among other diseases including pain, inflammation, and cancer. However, the lack of specific inhibitors hinders the study of TRPM2 in brain pathophysiology. Here, we present the design of a novel TRPM2 antagonist, tatM2NX, which prevents ligand binding and TRPM2 activation. We used mutagenesis of tatM2NX to determine the structure-activity relationship and antagonistic mechanism on TRPM2 using whole-cell patch clamp and Calcium imaging in human embryonic kidney 293 cells with stable human TRPM2 expression. We show that tatM2NX inhibits over 90% of TRPM2 channel currents at concentrations as low as 2 μM. Moreover, tatM2NX is a potent antagonist with an IC50 of 396 nM. Our results from tatM2NX mutagenesis indicate that specific residues within the tatM2NX C terminus are required to confer antagonism on TRPM2. Therefore, the peptide tatM2NX represents a new tool for the study of TRPM2 function in cell biology and enhances our understanding of TRPM2 in disease. SIGNIFICANCE STATEMENT: TatM2NX is a potent TRPM2 channel antagonist with the potential for clinical benefit in neurological diseases. This study characterizes interactions of tatM2NX with TRPM2 and the mechanism of action using structure-activity analysis.
Collapse
Affiliation(s)
- I Cruz-Torres
- Departments of Pharmacology (I.C.-T., P.S.H.) and Anesthesiology (P.S.H.) and Neuronal Injury & Plasticity Program (I.C.-T., P.S.H.), University of Colorado School of Medicine, Aurora, Colorado; and Department of Pharmaceutical Sciences, University of Colorado Skaggs School of Pharmacy and Pharmaceutical Sciences, Aurora, Colorado (D.S.B.)
| | - D S Backos
- Departments of Pharmacology (I.C.-T., P.S.H.) and Anesthesiology (P.S.H.) and Neuronal Injury & Plasticity Program (I.C.-T., P.S.H.), University of Colorado School of Medicine, Aurora, Colorado; and Department of Pharmaceutical Sciences, University of Colorado Skaggs School of Pharmacy and Pharmaceutical Sciences, Aurora, Colorado (D.S.B.)
| | - P S Herson
- Departments of Pharmacology (I.C.-T., P.S.H.) and Anesthesiology (P.S.H.) and Neuronal Injury & Plasticity Program (I.C.-T., P.S.H.), University of Colorado School of Medicine, Aurora, Colorado; and Department of Pharmaceutical Sciences, University of Colorado Skaggs School of Pharmacy and Pharmaceutical Sciences, Aurora, Colorado (D.S.B.)
| |
Collapse
|
110
|
Islam MJ, Khan AM, Parves MR, Hossain MN, Halim MA. Prediction of Deleterious Non-synonymous SNPs of Human STK11 Gene by Combining Algorithms, Molecular Docking, and Molecular Dynamics Simulation. Sci Rep 2019; 9:16426. [PMID: 31712642 PMCID: PMC6848484 DOI: 10.1038/s41598-019-52308-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 10/09/2019] [Indexed: 02/08/2023] Open
Abstract
Serine-threonine kinase11 (STK11) is a tumor suppressor gene which plays a key role in regulating cell growth and apoptosis. It is widely known as a multitasking kinase and engaged in cell polarity, cell cycle arrest, chromatin remodeling, energy metabolism, and Wnt signaling. The substitutions of single amino acids in highly conserved regions of the STK11 protein are associated with Peutz-Jeghers syndrome (PJS), which is an autosomal dominant inherited disorder. The abnormal function of the STK11 protein is still not well understood. In this study, we classified disease susceptible single nucleotide polymorphisms (SNPs) in STK11 by using different computational algorithms. We identified the deleterious nsSNPs, constructed mutant protein structures, and evaluated the impact of mutation by employing molecular docking and molecular dynamics analysis. Our results show that W239R and W308C variants are likely to be highly deleterious mutations found in the catalytic kinase domain, which may destabilize structure and disrupt the activation of the STK11 protein as well as reduce its catalytic efficiency. The W239R mutant is likely to have a greater impact on destabilizing the protein structure compared to the W308C mutant. In conclusion, these mutants can help to further realize the large pool of disease susceptibilities linked with catalytic kinase domain activation of STK11 and assist to develop an effective drug for associated diseases.
Collapse
Affiliation(s)
- Md Jahirul Islam
- Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, 218 Elephant Road, Dhaka, 1205, Bangladesh
- Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong (USTC), Foy's Lake, Khulshi- 4202, Chittagong, Bangladesh
| | - Akib Mahmud Khan
- Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, 218 Elephant Road, Dhaka, 1205, Bangladesh
| | - Md Rimon Parves
- Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong (USTC), Foy's Lake, Khulshi- 4202, Chittagong, Bangladesh
| | - Md Nayeem Hossain
- Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, 218 Elephant Road, Dhaka, 1205, Bangladesh
| | - Mohammad A Halim
- Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, 218 Elephant Road, Dhaka, 1205, Bangladesh.
| |
Collapse
|
111
|
Computational Tools in the Discovery of FABP4 Ligands: A Statistical and Molecular Modeling Approach. Mar Drugs 2019; 17:md17110624. [PMID: 31683588 PMCID: PMC6891735 DOI: 10.3390/md17110624] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 10/17/2019] [Accepted: 10/29/2019] [Indexed: 12/12/2022] Open
Abstract
Small molecule inhibitors of adipocyte fatty-acid binding protein 4 (FABP4) have received interest following the recent publication of their pharmacologically beneficial effects. Recently, it was revealed that FABP4 is an attractive molecular target for the treatment of type 2 diabetes, other metabolic diseases, and some type of cancers. In past years, hundreds of effective FABP4 inhibitors have been synthesized and discovered, but, unfortunately, none have reached the clinical research phase. The field of computer-aided drug design seems to be promising and useful for the identification of FABP4 inhibitors; hence, different structure- and ligand-based computational approaches have been used for their identification. In this paper, we searched for new potentially active FABP4 ligands in the Marine Natural Products (MNP) database. We retrieved 14,492 compounds from this database and filtered through them with a statistical and computational filter. Seven compounds were suggested by our methodology to possess a potential inhibitory activity upon FABP4 in the range of 97–331 nM. ADMET property prediction was performed to validate the hypothesis of the interaction with the intended target and to assess the drug-likeness of these derivatives. From these analyses, three molecules that are excellent candidates for becoming new drugs were found.
Collapse
|
112
|
Interactions of a short hyaluronan chain with a phospholipid membrane. Colloids Surf B Biointerfaces 2019; 184:110539. [PMID: 31629183 DOI: 10.1016/j.colsurfb.2019.110539] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 09/09/2019] [Accepted: 09/29/2019] [Indexed: 01/06/2023]
Abstract
Hyaluronic acid and phospholipids are two components that are present in the synovial fluid, and both are implicated as important facilitators of joint lubrication. In this work we aim to clarify how hyaluronic acid interacts with a phospholipid bilayer through their molecular interactions at the bilayer surface. To this end we performed molecular dynamics simulations of one hyaluronic acid molecule at a phospholipid bilayer in aqueous solution. The simulations were carried out for two aqueous solutions of equal concentrations, containing either NaCl or CaCl2. We analyzed hydrogen bonds, hydrophobic contacts and cation mediated bridges to clarify how hyaluoronic acid binds to a phospholipid bilayer. The analysis shows that calcium ions promote longer lasting bonds between the species as they create calcium ion bridges between the carboxylate group of hyaluronic acid and the phosphate group of the phospholipid. This type of additional bonding does not significantly influence the total number of contact created, but rather stabilizes the contact. The presented results can facilitate understanding of the role of hyaluronic acid and phospholipid interactions in terms of lubrication of articular cartilage.
Collapse
|
113
|
Tietze D, Kaufmann D, Tietze AA, Voll A, Reher R, König G, Hausch F. Structural and Dynamical Basis of G Protein Inhibition by YM-254890 and FR900359: An Inhibitor in Action. J Chem Inf Model 2019; 59:4361-4373. [PMID: 31539242 DOI: 10.1021/acs.jcim.9b00433] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Specific inhibition of G proteins holds a great pharmacological promise to, e.g., target oncogenic Gq/11 proteins and can be achieved by the two natural products FR900359 (FR) and YM-254890 (YM). Unfortunately, recent rational-design-based approaches to address G proteins other than Gq/11/14 subtypes were not successful mainly due to the conformational complexity of these new modalities-like compounds. Here, we report the water-derived NMR structure of YM, which strongly differs from the conformation of Gq-bound YM as found in the crystal structure. Reanalysis of the crystal structure suggests that the water-derived NMR structure of YM also represents a valid solution of the electron density. Extensive molecular dynamic simulations unveiled much higher binding affinities of the water-derived NMR structure compared to the original YM conformation of pdb 3ah8 . Employing a in-silico-designed, fast activating G protein conformation molecular dynamics data ultimately show how the inhibitor impairs the domain motion of the G protein necessary to hinder nucleotide exchange.
Collapse
Affiliation(s)
- Daniel Tietze
- Eduard-Zintl-Institute for Inorganic and Physical Chemistry , Darmstadt University of Technology , Alarich-Weiss-Strasse 8 , 64287 Darmstadt , Germany.,Department of Chemistry and Molecular Biology, Wallenberg Centre for Molecular and Translational Medicine , University of Gothenburg , Kemigården 4 , 412 96 Göteborg , Sweden
| | - Desireé Kaufmann
- Eduard-Zintl-Institute for Inorganic and Physical Chemistry , Darmstadt University of Technology , Alarich-Weiss-Strasse 8 , 64287 Darmstadt , Germany
| | - Alesia A Tietze
- Department of Chemistry and Molecular Biology, Wallenberg Centre for Molecular and Translational Medicine , University of Gothenburg , Kemigården 4 , 412 96 Göteborg , Sweden
| | - Andreas Voll
- Clemens Schöpf Institute for Organic Chemistry and Biochemistry , Darmstadt University of Technology , Alarich-Weiss-Strasse 4 , 64287 Darmstadt , Germany
| | - Raphael Reher
- Institute for Pharmaceutical Biology , University of Bonn , Nussallee 6 , 53115 Bonn , Germany
| | - Gabriele König
- Institute for Pharmaceutical Biology , University of Bonn , Nussallee 6 , 53115 Bonn , Germany
| | - Felix Hausch
- Clemens Schöpf Institute for Organic Chemistry and Biochemistry , Darmstadt University of Technology , Alarich-Weiss-Strasse 4 , 64287 Darmstadt , Germany
| |
Collapse
|
114
|
Fährrolfes R, Bietz S, Flachsenberg F, Meyder A, Nittinger E, Otto T, Volkamer A, Rarey M. ProteinsPlus: a web portal for structure analysis of macromolecules. Nucleic Acids Res 2019; 45:W337-W343. [PMID: 28472372 PMCID: PMC5570178 DOI: 10.1093/nar/gkx333] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 04/18/2017] [Indexed: 11/15/2022] Open
Abstract
With currently more than 126 000 publicly available structures and an increasing growth rate, the Protein Data Bank constitutes a rich data source for structure-driven research in fields like drug discovery, crop science and biotechnology in general. Typical workflows in these areas involve manifold computational tools for the analysis and prediction of molecular functions. Here, we present the ProteinsPlus web server that offers a unified easy-to-use interface to a broad range of tools for the early phase of structure-based molecular modeling. This includes solutions for commonly required pre-processing tasks like structure quality assessment (EDIA), hydrogen placement (Protoss) and the search for alternative conformations (SIENA). Beyond that, it also addresses frequent problems as the generation of 2D-interaction diagrams (PoseView), protein-protein interface classification (HyPPI) as well as automatic pocket detection and druggablity assessment (DoGSiteScorer). The unified ProteinsPlus interface covering all featured approaches provides various facilities for intuitive input and result visualization, case-specific parameterization and download options for further processing. Moreover, its generalized workflow allows the user a quick familiarization with the different tools. ProteinsPlus also stores the calculated results temporarily for future request and thus facilitates convenient result communication and re-access. The server is freely available at http://proteins.plus.
Collapse
Affiliation(s)
- Rainer Fährrolfes
- Universität Hamburg, ZBH-Center for Bioinformatics, Bundesstrasse 43, 20146 Hamburg, Germany
| | - Stefan Bietz
- Universität Hamburg, ZBH-Center for Bioinformatics, Bundesstrasse 43, 20146 Hamburg, Germany
| | - Florian Flachsenberg
- Universität Hamburg, ZBH-Center for Bioinformatics, Bundesstrasse 43, 20146 Hamburg, Germany
| | - Agnes Meyder
- Universität Hamburg, ZBH-Center for Bioinformatics, Bundesstrasse 43, 20146 Hamburg, Germany
| | - Eva Nittinger
- Universität Hamburg, ZBH-Center for Bioinformatics, Bundesstrasse 43, 20146 Hamburg, Germany
| | - Thomas Otto
- Universität Hamburg, ZBH-Center for Bioinformatics, Bundesstrasse 43, 20146 Hamburg, Germany
| | - Andrea Volkamer
- Institute of Physiology, Charité-Universitätsmedizin Berlin, Virchowweg 6, 10117 Berlin, Germany
| | - Matthias Rarey
- Universität Hamburg, ZBH-Center for Bioinformatics, Bundesstrasse 43, 20146 Hamburg, Germany
| |
Collapse
|
115
|
Bełdowski P, Mazurkiewicz A, Topoliński T, Małek T. Hydrogen and Water Bonding between Glycosaminoglycans and Phospholipids in the Synovial Fluid: Molecular Dynamics Study. MATERIALS (BASEL, SWITZERLAND) 2019; 12:E2060. [PMID: 31252519 PMCID: PMC6651827 DOI: 10.3390/ma12132060] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 06/24/2019] [Accepted: 06/25/2019] [Indexed: 11/17/2022]
Abstract
Synovial fluid is a lubricant of the synovial joint that shows remarkable tribological properties. These properties originate in the synergy between its components, with two of its major components, glycosaminoglycans (GAGs) and phospholipids (PLs), playing a major role in boundary and mixed lubrication regimes. All-atom molecular dynamic simulations were performed to investigate the way these components bond. Hyaluronic acid (HA) and chondroitin sulphate (CS) bonding with three types of lipids was tested. The results show that both glycosaminoglycans bind lipids at a similar rate, except for 1,2-d-ipalmitoyl-sn-glycero-3-phosphoethanolamine lipids, which bind to chondroitin at a much higher rate than to hyaluronan. The results suggest that different synovial fluid lipids may play a different role when binding to both hyaluronan and chondroitin sulphate. The presented results may help in understanding a process of lubrication of articular cartilage at a nanoscale level.
Collapse
Affiliation(s)
- Piotr Bełdowski
- Institute for Multiscale Simulation, Cluster of Excellence "Engineering of Advanced Materials", Friedrich-Alexander-Universität Erlangen-Nürnberg, Cauerstrasse 3, 91058 Erlangen, Germany
- Institute of Mathematics and Physics, UTP University of Science and Technology, Kaliskiego 7 Street, 85-796 Bydgoszcz, Poland
| | - Adam Mazurkiewicz
- Mechanical Engineering Department, UTP University of Science and Technology, Kaliskiego 7 Street, 85-796 Bydgoszcz, Poland.
| | - Tomasz Topoliński
- Mechanical Engineering Department, UTP University of Science and Technology, Kaliskiego 7 Street, 85-796 Bydgoszcz, Poland
| | - Tomasz Małek
- Student Scientific Club "BioMed", Mechanical Engineering Department, UTP University of Science and Technology, Kaliskiego 7 Street, 85-796 Bydgoszcz, Poland
| |
Collapse
|
116
|
Assessment of structurally and functionally high-risk nsSNPs impacts on human bone morphogenetic protein receptor type IA (BMPR1A) by computational approach. Comput Biol Chem 2019; 80:31-45. [DOI: 10.1016/j.compbiolchem.2019.03.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 11/13/2018] [Accepted: 03/11/2019] [Indexed: 12/15/2022]
|
117
|
Gonzalez TL, Moos RK, Gersch CL, Johnson MD, Richardson RJ, Koch HM, Rae JM. Metabolites of n-Butylparaben and iso-Butylparaben Exhibit Estrogenic Properties in MCF-7 and T47D Human Breast Cancer Cell Lines. Toxicol Sci 2019; 164:50-59. [PMID: 29945225 DOI: 10.1093/toxsci/kfy063] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Two oxidized metabolites of n-butylparaben (BuP) and iso-butylparaben (IsoBuP) discovered in human urine samples exhibit structural similarity to endogenous estrogens. We hypothesized that these metabolites bind to the human estrogen receptor (ER) and promote estrogen signaling. We tested this using models of ER-mediated cellular proliferation. The estrogenic properties of 3-hydroxy n-butyl 4-hydroxybenzoate (3OH) and 2-hydroxy iso-butyl 4-hydroxybenzoate (2OH) were determined using the ER-positive, estrogen-dependent human breast cancer cell lines MCF-7, and T47D. The 3OH metabolite induced cellular proliferation with EC50 of 8.2 µM in MCF-7 cells. The EC50 for 3OH in T47D cells could not be reached. The 2OH metabolite induced proliferation with EC50 of 2.2 µM and 43.0 µM in MCF-7 and T47D cells, respectively. The EC50 for the parental IsoBuP and BuP was 0.30 and 1.2 µM in MCF-7 cells, respectively. The expression of a pro-proliferative, estrogen-inducible gene (GREB1) was induced by these compounds and blocked by co-administration of an ER antagonist (ICI 182, 780), confirming the ER-dependence of these effects. The metabolites promoted significant ER-dependent transcriptional activity of an ERE-luciferase reporter construct at 10 and 20 µM for 2OH and 10 µM for 3OH. Computational docking studies showed that the paraben compounds exhibited the potential for favorable ligand-binding domain interactions with human ERα in a manner similar to known x-ray crystal structures of 17ß-estradiol in complex with ERα. We conclude that the hydroxylated metabolites of BuP and IsoBuP are weak estrogens and should be considered as additional components of potential endocrine disrupting effects upon paraben exposure.
Collapse
Affiliation(s)
- Thomas L Gonzalez
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109
| | - Rebecca K Moos
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr Universität Bochum (IPA), Bochum 44789, Germany
| | - Christina L Gersch
- Division of Hematology/Oncology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Michael D Johnson
- Department of Oncology, Georgetown University School of Medicine, Washington, District of Columbia 20057
| | - Rudy J Richardson
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109.,Department of Neurology, University of Michigan, Ann Arbor, Michigan 48109
| | - Holger M Koch
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr Universität Bochum (IPA), Bochum 44789, Germany
| | - James M Rae
- Division of Hematology/Oncology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109
| |
Collapse
|
118
|
Gonzalez TL, Rae JM, Colacino JA, Richardson RJ. Homology models of mouse and rat estrogen receptor- α ligand-binding domain created by in silico mutagenesis of a human template: molecular docking with 17ß-estradiol, diethylstilbestrol, and paraben analogs. COMPUTATIONAL TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2019; 10:1-16. [PMID: 30740556 PMCID: PMC6363358 DOI: 10.1016/j.comtox.2018.11.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Crystal structures exist for human, but not rodent, estrogen receptor-α ligand-binding domain (ERα-LBD). Consequently, rodent studies involving binding of compounds to ERα-LBD are limited in their molecular-level interpretation and extrapolation to humans. Because the sequences of rodent and human ERα-LBDs are > 95% identical, we expected their 3D structures and ligand binding to be highly similar. To test this hypothesis, we used the human ERα-LBD structure (PDB 3UUD) as a template to produce rat and mouse homology models. Employing the rodent models and human structure, we generated docking poses of 23 Group A ligands (17ß-estradiol, diethylstilbestrol, and 21 paraben analogs) in AutoDock Vina for interspecies comparisons. Ligand RMSDs (Å) (median, 95% CI) were 0.49 (0.21-1.82) (human-mouse) and 1.19 (0.22-1.82) (human-rat), well below the 2.0-2.5 Å range for equivalent docking poses. Numbers of interspecies ligand-receptor residue contacts were highly similar, with Sorensen Sc (%) = 96.8 (90.0-100) (human-mouse) and 97.7 (89.5-100) (human-rat). Likewise, numbers of interspecies ligand-receptor residue contacts were highly correlated: Pearson r = 0.913 (human-mouse) and 0.925 (human-rat). Numbers of interspecies ligand-receptor atom contacts were even more tightly correlated: r = 0.979 (human-mouse) and 0.986 (human-rat). Pyramid plots of numbers of ligand-receptor atom contacts by residue exhibited high interspecies symmetry and had Spearman r s = 0.977 (human-mouse) and 0.966 (human-rat). Group B ligands included 15 ring-substituted parabens recently shown experimentally to exhibit decreased binding to human ERα and to exert increased antimicrobial activity. Ligand efficiencies calculated from docking ligands into human ERα-LBD were well correlated with those derived from published experimental data (Pearson partial r p = 0.894 and 0.918; Groups A and B, respectively). Overall, the results indicate that our constructed rodent ERα-LBDs interact with ligands in like manner to the human receptor, thus providing a high level of confidence in extrapolations of rodent to human ligand-receptor interactions.
Collapse
Affiliation(s)
- Thomas L. Gonzalez
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - James M. Rae
- Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Justin A. Colacino
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109 USA
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109 USA
| | - Rudy J. Richardson
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109 USA
- Department of Neurology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| |
Collapse
|
119
|
In Silico Analysis of the Subtype Selective Blockage of KCNA Ion Channels through the µ-Conotoxins PIIIA, SIIIA, and GIIIA. Mar Drugs 2019; 17:md17030180. [PMID: 30893914 PMCID: PMC6471588 DOI: 10.3390/md17030180] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 03/12/2019] [Accepted: 03/15/2019] [Indexed: 12/12/2022] Open
Abstract
Understanding subtype specific ion channel pore blockage by natural peptide-based toxins is crucial for developing such compounds into promising drug candidates. Herein, docking and molecular dynamics simulations were employed in order to understand the dynamics and binding states of the µ-conotoxins, PIIIA, SIIIA, and GIIIA, at the voltage-gated potassium channels of the KV1 family, and they were correlated with their experimental activities recently reported by Leipold et al. Their different activities can only adequately be understood when dynamic information about the toxin-channel systems is available. For all of the channel-bound toxins investigated herein, a certain conformational flexibility was observed during the molecular dynamic simulations, which corresponds to their bioactivity. Our data suggest a similar binding mode of µ-PIIIA at KV1.6 and KV1.1, in which a plethora of hydrogen bonds are formed by the Arg and Lys residues within the α-helical core region of µ-PIIIA, with the central pore residues of the channel. Furthermore, the contribution of the K+ channel’s outer and inner pore loops with respect to the toxin binding. and how the subtype specificity is induced, were proposed.
Collapse
|
120
|
Identification and structural characterization of deleterious non-synonymous single nucleotide polymorphisms in the human SKP2 gene. Comput Biol Chem 2019; 79:127-136. [PMID: 30802828 DOI: 10.1016/j.compbiolchem.2019.02.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 01/27/2019] [Accepted: 02/13/2019] [Indexed: 12/17/2022]
Abstract
In SCF (Skp, Cullin, F-box) ubiquitin-protein ligase complexes, S-phase kinase 2 (SKP2) is one of the major players of F-box family, that is responsible for the degradation of several important cell regulators and tumor suppressor proteins. Despite of having significant evidence for the role of SKP2 on tumorgenesis, there is a lack of available data regarding the effect of non-synonymous polymorphisms. In this communication, the structural and functional consequences of non-synonymous single nucleotide polymorphisms (nsSNPs) of SKP2 have been reported by employing various computational approaches and molecular dynamics simulation. Initially, several computational tools like SIFT, PolyPhen-2, PredictSNP, I-Mutant 2.0 and ConSurf have been implicated in this study to explore the damaging SNPs. In total of 172 nsSNPs, 5 nsSNPs were identified as deleterious and 3 of them were predicted to be decreased the stability of protein. Guided from ConSurf analysis, P101L (rs761253702) and Y346C (rs755010517) were categorized as the highly conserved and functional disrupting mutations. Therefore, these mutations were subjected to three dimensional model building and molecular dynamics simulation study for the detailed structural consequences upon the mutations. The study revealed that P101L and Y346C mutations increased the flexibility and changed the structural dynamics. As both these mutations are located in the most functional regions of SKP2 protein, these computational insights might be helpful to consider these nsSNPs for wet-lab confirmatory analysis as well as in rationalizing future population based studies and structure based drug design against SKP2.
Collapse
|
121
|
Jukič M, Rožman K, Sova M, Barreteau H, Gobec S. Anthranilic Acid Inhibitors of Undecaprenyl Pyrophosphate Synthase (UppS), an Essential Enzyme for Bacterial Cell Wall Biosynthesis. Front Microbiol 2019; 9:3322. [PMID: 30692977 PMCID: PMC6339874 DOI: 10.3389/fmicb.2018.03322] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 12/20/2018] [Indexed: 12/17/2022] Open
Abstract
We report the successful implementation of virtual screening in the discovery of new inhibitors of undecaprenyl pyrophosphate synthase (UppS) from Escherichia coli. UppS is an essential enzyme in the biosynthesis of bacterial cell wall. It catalyzes the condensation of farnesyl pyrophosphate (FPP) with eight consecutive isopentenyl pyrophosphate units (IPP), in which new cis-double bonds are formed, to generate undecaprenyl pyrophosphate. The latter serves as a lipid carrier for peptidoglycan synthesis, thus representing an important target in the antibacterial drug design. A pharmacophore model was designed on a known bisphosphonate BPH-629 and used to prepare an enriched compound library that was further docked into UppS conformational ensemble generated by molecular dynamics experiment. The docking resulted in three anthranilic acid derivatives with promising inhibitory activity against UppS. Compound 2 displayed high inhibitory potency (IC50 = 25 μM) and good antibacterial activity against E. coli BW25113 ΔtolC strain (MIC = 0.5 μg/mL).
Collapse
Affiliation(s)
- Marko Jukič
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Kaja Rožman
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Matej Sova
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Hélène Barreteau
- Bacterial Cell Envelopes and Antibiotics Group, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| |
Collapse
|
122
|
The proton and metal binding sites responsible for the pH-dependent green-red bioluminescence color tuning in firefly luciferases. Sci Rep 2018; 8:17594. [PMID: 30514851 PMCID: PMC6279810 DOI: 10.1038/s41598-018-33252-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 09/19/2018] [Indexed: 11/17/2022] Open
Abstract
Firefly luciferases produce yellow-green light under physiological and alkaline conditions, however at acidic pH, higher temperatures or in the presence of heavy metals the color changes to red, a property called pH-sensitivity. Despite many decades of studies, the proton and metal binding sites responsible for pH-sensitivity remain enigmatic. Previously we suggested that the salt bridge E311/R337 keeps a closed conformation of the luciferin phenolate binding site. Here we further investigated the effect of this salt bridge and mutations of the neighbor residues H310 and E/N354, on metal and pH-sensitivity of firefly luciferases emitting distinct bioluminescence colors (Cratomorphus distinctus: 548 nm; Macrolampis sp2: 569 nm). The substitutions of H310 and E/N354 modulate metal sensitivity, whereas the carboxylate of E311 may work as the catalytic base essential for green bioluminescence and pH-sensitivity. Modeling studies showed that H310, E311 and E354 side-chains coordinate Zinc, constituting the metal binding site and the pH-sensor. Electrostatic potential and pKa calculations suggest that the external couple H310/E354 is affected by pH, whereas E311/R337 make a stabilized internal pair which retains excited oxyluciferin ejected proton near its phenolate group into a high energy state, promoting yellow-green bioluminescence. Protonation or metal binding weaken these electrostatic gates and their ability to retain the excited oxyluciferin released proton near its phenolate, promoting red light emission.
Collapse
|
123
|
Pulido D, Sharma U, Vadon-Le Goff S, Hussain SA, Cordes S, Mariano N, Bettler E, Moali C, Aghajari N, Hohenester E, Hulmes DJS. Structural Basis for the Acceleration of Procollagen Processing by Procollagen C-Proteinase Enhancer-1. Structure 2018; 26:1384-1392.e3. [PMID: 30078642 PMCID: PMC6372009 DOI: 10.1016/j.str.2018.06.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 06/18/2018] [Accepted: 06/28/2018] [Indexed: 11/06/2022]
Abstract
Procollagen C-proteinase enhancer-1 (PCPE-1) is a secreted protein that specifically accelerates proteolytic release of the C-propeptides from fibrillar procollagens, a crucial step in fibril assembly. As such, it is a potential therapeutic target to improve tissue repair and prevent fibrosis, a major cause of mortality worldwide. Here we present the crystal structure of the active CUB1CUB2 fragment of PCPE-1 bound to the C-propeptide trimer of procollagen III (CPIII). This shows that the two CUB domains bind to two different chains of CPIII and that the N-terminal region of one CPIII chain, close to the proteolytic cleavage site, lies in the cleft between CUB1 and CUB2. This suggests that enhancing activity involves unraveling of this chain from the rest of the trimer, thus facilitating the action of the proteinase involved. Support for this hypothesis comes from site-directed mutagenesis, enzyme assays, binding studies, and molecular modeling. The crystal structure of PCPE-1 bound to the C-propeptides has been determined The N terminus of one propeptide chain binds to the CUB1CUB2 fragment of PCPE-1 PCPE-1 seems to unravel the propeptide trimer to enable proteolytic release Molecular modeling with the proteinase and its substrate supports this hypothesis
Collapse
Affiliation(s)
- David Pulido
- Department of Life Sciences, Imperial College, London SW7 2AZ, UK
| | - Urvashi Sharma
- UMR5086, CNRS/Université Claude Bernard Lyon 1, 69367 Lyon Cedex 7, France
| | | | | | - Sarah Cordes
- Department of Life Sciences, Imperial College, London SW7 2AZ, UK
| | - Natacha Mariano
- UMR5305, CNRS/Université Claude Bernard Lyon 1, 69367 Lyon Cedex 7, France
| | - Emmanuel Bettler
- UMR5305, CNRS/Université Claude Bernard Lyon 1, 69367 Lyon Cedex 7, France
| | - Catherine Moali
- UMR5305, CNRS/Université Claude Bernard Lyon 1, 69367 Lyon Cedex 7, France
| | - Nushin Aghajari
- UMR5086, CNRS/Université Claude Bernard Lyon 1, 69367 Lyon Cedex 7, France
| | | | - David J S Hulmes
- Department of Life Sciences, Imperial College, London SW7 2AZ, UK; UMR5305, CNRS/Université Claude Bernard Lyon 1, 69367 Lyon Cedex 7, France.
| |
Collapse
|
124
|
De Luca L, Ferro S, Buemi MR, Monforte AM, Gitto R, Schirmeister T, Maes L, Rescifina A, Micale N. Discovery of benzimidazole-based Leishmania mexicana cysteine protease CPB2.8ΔCTE inhibitors as potential therapeutics for leishmaniasis. Chem Biol Drug Des 2018; 92:1585-1596. [PMID: 29729080 DOI: 10.1111/cbdd.13326] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Revised: 02/22/2018] [Accepted: 04/15/2018] [Indexed: 02/07/2023]
Abstract
Chemotherapy is currently the only effective approach to treat all forms of leishmaniasis. However, its effectiveness is severely limited due to high toxicity, long treatment length, drug resistance, or inadequate mode of administration. As a consequence, there is a need to identify new molecular scaffolds and targets as potential therapeutics for the treatment of this disease. We report a small series of 1,2-substituted-1H-benzo[d]imidazole derivatives (9a-d) showing affinity in the submicromolar range (Ki = 0.15-0.69 μM) toward Leishmania mexicanaCPB2.8ΔCTE, one of the more promising targets for antileishmanial drug design. The compounds confirmed activity in vitro against intracellular amastigotes of Leishmania infantum with the best result being obtained with derivative 9d (IC50 = 6.8 μM), although with some degree of cytotoxicity (CC50 = 8.0 μM on PMM and CC50 = 32.0 μM on MCR-5). In silico molecular docking studies and ADME-Tox properties prediction were performed to validate the hypothesis of the interaction with the intended target and to assess the drug-likeness of these derivatives.
Collapse
Affiliation(s)
- Laura De Luca
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Stefania Ferro
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Maria Rosa Buemi
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Anna-Maria Monforte
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Rosaria Gitto
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Tanja Schirmeister
- Institute of Pharmacy and Biochemistry, University of Mainz, Mainz, Germany
| | - Louis Maes
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Antwerp, Belgium
| | | | - Nicola Micale
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| |
Collapse
|
125
|
Höck H, Engel S, Weingarten S, Keul H, Schwaneberg U, Möller M, Bocola M. Comparison of Candida antarctica Lipase B Variants for Conversion of ε-Caprolactone in Aqueous Medium-Part 2. Polymers (Basel) 2018; 10:E524. [PMID: 30966558 PMCID: PMC6415414 DOI: 10.3390/polym10050524] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 04/26/2018] [Accepted: 05/10/2018] [Indexed: 12/22/2022] Open
Abstract
Enzyme-catalyzed ring-opening polymerization of lactones is a method of increasing interest for the synthesis of polyesters. In the present work, we investigated which changes in the structure of Candida antarctica lipase B (CaLB) shift the catalytic equilibrium between esterification and hydrolysis towards polymerization. Therefore, we present two concepts: (i) removing the glycosylation of CaLB to increase the surface hydrophobicity; and (ii) introducing a hydrophobic lid adapted from Pseudomonas cepacia lipase (PsCL) to enhance the interaction of a growing polymer chain to the elongated lid helix. The deglycosylated CaLB (CaLB-degl) was successfully generated by site-saturation mutagenesis of asparagine 74. Furthermore, computational modeling showed that the introduction of a lid helix at position Ala148 was structurally feasible and the geometry of the active site remained intact. Via overlap extension PCR the lid was successfully inserted, and the variant was produced in large scale in Pichia pastoris with glycosylation (CaLB-lid) and without (CaLB-degl-lid). While the lid variants show a minor positive effect on the polymerization activity, CaLB-degl showed a clearly reduced hydrolytic and enhanced polymerization activity. Immobilization in a hydrophobic polyglycidol-based microgel intensified this effect such that a higher polymerization activity was achieved, compared to the "gold standard" Novozym® 435.
Collapse
Affiliation(s)
- Heidi Höck
- DWI-Leibniz Institute for Interactive Materials and Institute of Biotechnology, RWTH Aachen University, Forckenbeckstraße 50, D-52056 Aachen, Germany.
| | - Stefan Engel
- DWI-Leibniz Institute for Interactive Materials and Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Forckenbeckstraße 50, D-52056 Aachen, Germany.
| | - Simone Weingarten
- DWI-Leibniz Institute for Interactive Materials and Institute of Biotechnology, RWTH Aachen University, Forckenbeckstraße 50, D-52056 Aachen, Germany.
| | - Helmut Keul
- DWI-Leibniz Institute for Interactive Materials and Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Forckenbeckstraße 50, D-52056 Aachen, Germany.
| | - Ulrich Schwaneberg
- DWI-Leibniz Institute for Interactive Materials and Institute of Biotechnology, RWTH Aachen University, Forckenbeckstraße 50, D-52056 Aachen, Germany.
| | - Martin Möller
- DWI-Leibniz Institute for Interactive Materials and Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Forckenbeckstraße 50, D-52056 Aachen, Germany.
| | - Marco Bocola
- DWI-Leibniz Institute for Interactive Materials and Institute of Biotechnology, RWTH Aachen University, Forckenbeckstraße 50, D-52056 Aachen, Germany.
| |
Collapse
|
126
|
Raschka S, Wolf AJ, Bemister-Buffington J, Kuhn LA. Protein–ligand interfaces are polarized: discovery of a strong trend for intermolecular hydrogen bonds to favor donors on the protein side with implications for predicting and designing ligand complexes. J Comput Aided Mol Des 2018; 32:511-528. [DOI: 10.1007/s10822-018-0105-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 02/05/2018] [Indexed: 10/18/2022]
|
127
|
Vistoli G, Pedretti A, Mazzolari A, Testa B. Approaching Pharmacological Space: Events and Components. Methods Mol Biol 2018; 1800:245-274. [PMID: 29934897 DOI: 10.1007/978-1-4939-7899-1_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
With a view to introducing the concept of pharmacological space and its potential applications in investigating and predicting the toxic mechanisms of xenobiotics, this opening chapter describes the logical relations between conformational behavior, physicochemical properties and binding spaces, which are seen as the three key elements composing the pharmacological space. While the concept of conformational space is routinely used to encode molecular flexibility, the concepts of property spaces and, particularly, of binding spaces are more innovative. Indeed, their descriptors can find fruitful applications (a) in describing the dynamic adaptability a given ligand experiences when inserted into a specific environment, and (b) in parameterizing the flexibility a ligand retains when bound to a biological target. Overall, these descriptors can conveniently account for the often disregarded entropic factors and as such they prove successful when inserted in ligand- or structure-based predictive models. Notably, and although binding space parameters can clearly be derived from MD simulations, the chapter will illustrate how docking calculations, despite their static nature, are able to evaluate ligand's flexibility by analyzing several poses for each ligand. Such an approach, which represents the founding core of the binding space concept, can find various applications in which the related descriptors show an impressive enhancing effect on the statistical performances of the resulting predictive models.
Collapse
Affiliation(s)
- Giulio Vistoli
- Dipartimento di Scienze Farmaceutiche Università degli Studi di Milano, Milan, Italy.
| | - Alessandro Pedretti
- Dipartimento di Scienze Farmaceutiche Università degli Studi di Milano, Milan, Italy
| | - Angelica Mazzolari
- Dipartimento di Scienze Farmaceutiche Università degli Studi di Milano, Milan, Italy
| | | |
Collapse
|
128
|
Amata E, Rescifina A, Prezzavento O, Arena E, Dichiara M, Pittalà V, Montilla-García Á, Punzo F, Merino P, Cobos EJ, Marrazzo A. (+)-Methyl (1R,2S)-2-{[4-(4-Chlorophenyl)-4-hydroxypiperidin-1-yl]methyl}-1-phenylcyclopropanecarboxylate [(+)-MR200] Derivatives as Potent and Selective Sigma Receptor Ligands: Stereochemistry and Pharmacological Properties. J Med Chem 2017; 61:372-384. [PMID: 29220177 DOI: 10.1021/acs.jmedchem.7b01584] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Methoxycarbonyl-1-phenyl-2-cyclopropylmethyl based derivatives cis-(+)-1a [cis-(+)-MR200], cis-(-)-1a [cis-(-)-MR201], and trans-(±)-1a [trans-(±)-MR204], have been identified as new potent sigma (σ) receptor ligands. In the present paper, novel enantiomerically pure analogues were synthesized and optimized for their σ receptor affinity and selectivity. Docking studies rationalized the results obtained in the radioligand binding assay. Absolute stereochemistry was unequivocally established by X-ray analysis of precursor trans-(+)-5a as camphorsulfonyl derivative 9. The most promising compound, trans-(+)-1d, showed remarkable selectivity over a panel of more than 15 receptors as well as good chemical and enzymatic stability in human plasma. An in vivo evaluation evidenced that trans-(+)-1d, in contrast to trans-(-)-1d, cis-(+)-1d, or cis-(-)-1d, which behave as σ1 antagonists, exhibited a σ1 agonist profile. These data clearly demonstrated that compound trans-(+)-1d, due to its σ1 agonist activity and favorable receptor selectivity and stability, provided an useful tool for the study of σ1 receptors.
Collapse
Affiliation(s)
- Emanuele Amata
- Dipartimento di Scienze del Farmaco, Università di Catania , Viale A. Doria 6, 95125 Catania, Italy
| | - Antonio Rescifina
- Dipartimento di Scienze del Farmaco, Università di Catania , Viale A. Doria 6, 95125 Catania, Italy
| | - Orazio Prezzavento
- Dipartimento di Scienze del Farmaco, Università di Catania , Viale A. Doria 6, 95125 Catania, Italy
| | - Emanuela Arena
- Dipartimento di Scienze del Farmaco, Università di Catania , Viale A. Doria 6, 95125 Catania, Italy
| | - Maria Dichiara
- Dipartimento di Scienze del Farmaco, Università di Catania , Viale A. Doria 6, 95125 Catania, Italy
| | - Valeria Pittalà
- Dipartimento di Scienze del Farmaco, Università di Catania , Viale A. Doria 6, 95125 Catania, Italy
| | - Ángeles Montilla-García
- Institute of Neuroscience and Department of Pharmacology, Faculty of Medicine, University of Granada , Avenida de Madrid 11, E-18012 Granada, Spain
| | - Francesco Punzo
- Dipartimento di Scienze del Farmaco, Università di Catania , Viale A. Doria 6, 95125 Catania, Italy
| | - Pedro Merino
- Laboratorio de Síntesis Asimétrica, Departamento de Síntesis y Estructura de Biomoléculas, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), Universidad de Zaragoza, CSIC , Campus San Francisco, E-50009 Zaragoza, Aragón, Spain
| | - Enrique J Cobos
- Institute of Neuroscience and Department of Pharmacology, Faculty of Medicine, University of Granada , Avenida de Madrid 11, E-18012 Granada, Spain
| | - Agostino Marrazzo
- Dipartimento di Scienze del Farmaco, Università di Catania , Viale A. Doria 6, 95125 Catania, Italy
| |
Collapse
|
129
|
Ando M, Fiesel FC, Hudec R, Caulfield TR, Ogaki K, Górka-Skoczylas P, Koziorowski D, Friedman A, Chen L, Dawson VL, Dawson TM, Bu G, Ross OA, Wszolek ZK, Springer W. The PINK1 p.I368N mutation affects protein stability and ubiquitin kinase activity. Mol Neurodegener 2017; 12:32. [PMID: 28438176 PMCID: PMC5404317 DOI: 10.1186/s13024-017-0174-z] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 04/14/2017] [Indexed: 01/24/2023] Open
Abstract
Background Mutations in PINK1 and PARKIN are the most common causes of recessive early-onset Parkinson’s disease (EOPD). Together, the mitochondrial ubiquitin (Ub) kinase PINK1 and the cytosolic E3 Ub ligase PARKIN direct a complex regulated, sequential mitochondrial quality control. Thereby, damaged mitochondria are identified and targeted to degradation in order to prevent their accumulation and eventually cell death. Homozygous or compound heterozygous loss of either gene function disrupts this protective pathway, though at different steps and by distinct mechanisms. While structure and function of PARKIN variants have been well studied, PINK1 mutations remain poorly characterized, in particular under endogenous conditions. A better understanding of the exact molecular pathogenic mechanisms underlying the pathogenicity is crucial for rational drug design in the future. Methods Here, we characterized the pathogenicity of the PINK1 p.I368N mutation on the clinical and genetic as well as on the structural and functional level in patients’ fibroblasts and in cell-based, biochemical assays. Results Under endogenous conditions, PINK1 p.I368N is expressed, imported, and N-terminally processed in healthy mitochondria similar to PINK1 wild type (WT). Upon mitochondrial damage, however, full-length PINK1 p.I368N is not sufficiently stabilized on the outer mitochondrial membrane (OMM) resulting in loss of mitochondrial quality control. We found that binding of PINK1 p.I368N to the co-chaperone complex HSP90/CDC37 is reduced and stress-induced interaction with TOM40 of the mitochondrial protein import machinery is abolished. Analysis of a structural PINK1 p.I368N model additionally suggested impairments of Ub kinase activity as the ATP-binding pocket was found deformed and the substrate Ub was slightly misaligned within the active site of the kinase. Functional assays confirmed the lack of Ub kinase activity. Conclusions Here we demonstrated that mutant PINK1 p.I368N can not be stabilized on the OMM upon mitochondrial stress and due to conformational changes in the active site does not exert kinase activity towards Ub. In patients’ fibroblasts, biochemical assays and by structural analyses, we unraveled two pathomechanisms that lead to loss of function upon mutation of p.I368N and highlight potential strategies for future drug development. Electronic supplementary material The online version of this article (doi:10.1186/s13024-017-0174-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Maya Ando
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Fabienne C Fiesel
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA.,Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, 32224, USA
| | - Roman Hudec
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Thomas R Caulfield
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA.,Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, 32224, USA
| | - Kotaro Ogaki
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Paulina Górka-Skoczylas
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland.,Institute of Genetics and Biotechnology, Faculty of Biology, Warsaw University, Warsaw, Poland
| | - Dariusz Koziorowski
- Department of Neurology, Faculty of Health Science, Medical University of Warsaw, Warsaw, Poland
| | - Andrzej Friedman
- Department of Neurology, Faculty of Health Science, Medical University of Warsaw, Warsaw, Poland
| | - Li Chen
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, 70130-2685, USA
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, 70130-2685, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, 70130-2685, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Guojun Bu
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA.,Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, 32224, USA
| | - Owen A Ross
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA.,Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, 32224, USA
| | | | - Wolfdieter Springer
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA. .,Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, 32224, USA.
| |
Collapse
|
130
|
Dash R, Das R, Junaid M, Akash MFC, Islam A, Hosen SZ. In silico-based vaccine design against Ebola virus glycoprotein. Adv Appl Bioinform Chem 2017; 10:11-28. [PMID: 28356762 PMCID: PMC5367765 DOI: 10.2147/aabc.s115859] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Ebola virus (EBOV) is one of the lethal viruses, causing more than 24 epidemic outbreaks to date. Despite having available molecular knowledge of this virus, no definite vaccine or other remedial agents have been developed yet for the management and avoidance of EBOV infections in humans. Disclosing this, the present study described an epitope-based peptide vaccine against EBOV, using a combination of B-cell and T-cell epitope predictions, followed by molecular docking and molecular dynamics simulation approach. Here, protein sequences of all glycoproteins of EBOV were collected and examined via in silico methods to determine the most immunogenic protein. From the identified antigenic protein, the peptide region ranging from 186 to 220 and the sequence HKEGAFFLY from the positions of 154-162 were considered the most potential B-cell and T-cell epitopes, correspondingly. Moreover, this peptide (HKEGAFFLY) interacted with HLA-A*32:15 with the highest binding energy and stability, and also a good conservancy of 83.85% with maximum population coverage. The results imply that the designed epitopes could manifest vigorous enduring defensive immunity against EBOV.
Collapse
Affiliation(s)
- Raju Dash
- Molecular Modeling and Drug Design Laboratory (MMDDL), Pharmacology Research Division, Bangladesh Council of Scientific and Industrial Research (BCSIR), Chittagong, Bangladesh
| | - Rasel Das
- Nanotechnology and Catalysis Research Center, University of Malaya, Kuala Lumpur, Malaysia
| | - Md Junaid
- Department of Pharmaceutical Sciences, North South University, Dhaka, Bangladesh
| | | | - Ashekul Islam
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chittagong, Bangladesh
| | - Sm Zahid Hosen
- Molecular Modeling and Drug Design Laboratory (MMDDL), Pharmacology Research Division, Bangladesh Council of Scientific and Industrial Research (BCSIR), Chittagong, Bangladesh
| |
Collapse
|
131
|
Weinrich T, Gränz M, Grünewald C, Prisner TF, Göbel MW. Synthesis of a Cytidine Phosphoramidite with Protected Nitroxide Spin Label for EPR Experiments with RNA. European J Org Chem 2016. [DOI: 10.1002/ejoc.201601174] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Timo Weinrich
- Institute of Organic Chemistry and Chemical Biology; Goethe-University Frankfurt; Max-von-Laue-Str. 7 60438 Frankfurt am Main Germany
| | - Markus Gränz
- Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance; Goethe-University Frankfurt; Max-von-Laue-Str. 7 60438 Frankfurt am Main Germany
| | - Christian Grünewald
- Institute of Organic Chemistry and Chemical Biology; Goethe-University Frankfurt; Max-von-Laue-Str. 7 60438 Frankfurt am Main Germany
| | - Thomas F. Prisner
- Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance; Goethe-University Frankfurt; Max-von-Laue-Str. 7 60438 Frankfurt am Main Germany
| | - Michael W. Göbel
- Institute of Organic Chemistry and Chemical Biology; Goethe-University Frankfurt; Max-von-Laue-Str. 7 60438 Frankfurt am Main Germany
| |
Collapse
|
132
|
Kalra S, Pradeep MA, Mohanty AK, Kaushik JK. Structural, Functional and Phylogenetic Analysis of Sperm Lysozyme-Like Proteins. PLoS One 2016; 11:e0166321. [PMID: 27832206 PMCID: PMC5104373 DOI: 10.1371/journal.pone.0166321] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 10/26/2016] [Indexed: 01/22/2023] Open
Abstract
Sperm lysozyme-like proteins belonging to c-type lysozyme family evolved in multiple forms. Lysozyme-like proteins, viz., LYZL2, LYZL3 or SLLP1, LYZL4, LYZL5 and LYZL6 are expressed in the testis of mammals. Not all members of LYZL family have been uniformly and unambiguously identified in the genome and proteome of mammals. Some studies suggested a role of SLLP1 and LYZL4 in fertilization; however, the function of other LYZL proteins is unknown. We identified all known forms of LYZL proteins in buffalo sperm by LC-MS/MS. Cloning and sequence analysis of the Lyzl cDNA showed 38-50% identity at amino acid level among the buffalo LYZL paralogs, complete conservation of eight cysteines and other signature sequences of c-type lysozyme family. Catalytic residues in SLLP1, LYZL4 and LYZL5 have undergone replacement. The substrate binding residues showed significant variation in LYZL proteins. Residues at sites 62, 101, 114 in LYZL4; 101 in SLLP1; 37, 62, and 101 in LYZL6 were more variable among diverse species. Sites 63 and 108 occupied by tryptophan were least tolerant to variation. Site 37 also showed lower tolerance to substitution in SLLP1, LYZL4 and LYZL5, but more variable in non-testicular lysozymes. Models of LYZL proteins were created by homology modeling and the substrate binding pockets were analyzed in term of binding energies and contacting residues of LYZL proteins with tri-N-acetylglucosamine (NAG)3 in the A-B-C and B-C-D binding mode. Except LYZL6, LYZL proteins did not show significant difference in binding energies in comparison to hen egg white lysozyme in the A-B-C mode. (NAG)3 binding energy in the B-C-D mode was higher by 1.3-2.2 kcal/mol than in A-B-C mode. Structural analysis indicated that (NAG)3 was involved in making more extensive interactions including hydrogen bonding with LYZL proteins in B-C-D mode than in A-B-C mode. Despite large sequence divergence among themselves and with respect to c-type lysozymes, substrate binding residues as well as hydrogen bonding network between (NAG)3 and proteins were mostly conserved. LYZL5 in buffalo and other mammalian species contained additional 10-12 amino acid sequence at c-terminal that matched with ankyrin repeat domain-containing protein 27. Phylogenetic analysis indicated LYZL2 to be most ancient among all the LYZL proteins and that the evolution of LYZL proteins occurred through several gene duplications preceding the speciation of mammals from other vertebrates as distant as reptiles and amphibians.
Collapse
Affiliation(s)
- Shalini Kalra
- BTIS Sub-DIC, Animal Biotechnology Centre, National Dairy Research Institute, Karnal, 132001, India
| | | | - Ashok K. Mohanty
- BTIS Sub-DIC, Animal Biotechnology Centre, National Dairy Research Institute, Karnal, 132001, India
| | - Jai K. Kaushik
- BTIS Sub-DIC, Animal Biotechnology Centre, National Dairy Research Institute, Karnal, 132001, India
| |
Collapse
|
133
|
Puschmann A, Fiesel FC, Caulfield TR, Hudec R, Ando M, Truban D, Hou X, Ogaki K, Heckman MG, James ED, Swanberg M, Jimenez-Ferrer I, Hansson O, Opala G, Siuda J, Boczarska-Jedynak M, Friedman A, Koziorowski D, Rudzińska-Bar M, Aasly JO, Lynch T, Mellick GD, Mohan M, Silburn PA, Sanotsky Y, Vilariño-Güell C, Farrer MJ, Chen L, Dawson VL, Dawson TM, Wszolek ZK, Ross OA, Springer W. Heterozygous PINK1 p.G411S increases risk of Parkinson's disease via a dominant-negative mechanism. Brain 2016; 140:98-117. [PMID: 27807026 PMCID: PMC5379862 DOI: 10.1093/brain/aww261] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 08/31/2016] [Accepted: 09/02/2016] [Indexed: 01/31/2023] Open
Abstract
See Gandhi and Plun-Favreau (doi:10.1093/aww320) for a scientific commentary on this article. Heterozygous mutations in recessive Parkinson’s disease genes have been postulated to increase disease risk. Puschmann et al. report a genetic association between heterozygous PINK1 p.G411S and Parkinson’s disease. They provide structural and functional explanations for a partial dominant-negative effect of the mutant protein, which impairs wild-type PINK1 activity through hetero-dimerization. See Gandhi and Plun-Favreau (doi:10.1093/aww320) for a scientific commentary on this article. It has been postulated that heterozygous mutations in recessive Parkinson’s genes may increase the risk of developing the disease. In particular, the PTEN-induced putative kinase 1 (PINK1) p.G411S (c.1231G>A, rs45478900) mutation has been reported in families with dominant inheritance patterns of Parkinson’s disease, suggesting that it might confer a sizeable disease risk when present on only one allele. We examined families with PINK1 p.G411S and conducted a genetic association study with 2560 patients with Parkinson’s disease and 2145 control subjects. Heterozygous PINK1 p.G411S mutations markedly increased Parkinson’s disease risk (odds ratio = 2.92, P = 0.032); significance remained when supplementing with results from previous studies on 4437 additional subjects (odds ratio = 2.89, P = 0.027). We analysed primary human skin fibroblasts and induced neurons from heterozygous PINK1 p.G411S carriers compared to PINK1 p.Q456X heterozygotes and PINK1 wild-type controls under endogenous conditions. While cells from PINK1 p.Q456X heterozygotes showed reduced levels of PINK1 protein and decreased initial kinase activity upon mitochondrial damage, stress-response was largely unaffected over time, as expected for a recessive loss-of-function mutation. By contrast, PINK1 p.G411S heterozygotes showed no decrease of PINK1 protein levels but a sustained, significant reduction in kinase activity. Molecular modelling and dynamics simulations as well as multiple functional assays revealed that the p.G411S mutation interferes with ubiquitin phosphorylation by wild-type PINK1 in a heterodimeric complex. This impairs the protective functions of the PINK1/parkin-mediated mitochondrial quality control. Based on genetic and clinical evaluation as well as functional and structural characterization, we established p.G411S as a rare genetic risk factor with a relatively large effect size conferred by a partial dominant-negative function phenotype.
Collapse
Affiliation(s)
- Andreas Puschmann
- 1 Lund University, Department of Clinical Sciences Lund, Neurology, Sweden .,2 Department of Neurology, Skåne University Hospital, Sweden.,3 Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Fabienne C Fiesel
- 3 Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | | | - Roman Hudec
- 3 Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Maya Ando
- 3 Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Dominika Truban
- 3 Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Xu Hou
- 3 Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Kotaro Ogaki
- 3 Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Michael G Heckman
- 4 Division of Biomedical Statistics and Informatics, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Elle D James
- 3 Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Maria Swanberg
- 5 Lund University, Department of Experimental Medical Science, Lund, Sweden
| | | | - Oskar Hansson
- 6 Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Lund University, Sweden.,7 Memory Clinic, Skåne University Hospital, Malmö, Sweden
| | - Grzegorz Opala
- 8 Department of Neurology, School of Medicine in Katowice, Medical University of Silesia, Katowice, Poland
| | - Joanna Siuda
- 8 Department of Neurology, School of Medicine in Katowice, Medical University of Silesia, Katowice, Poland
| | | | | | | | | | - Jan O Aasly
- 10 Department of Neurology, St. Olav's Hospital, and Department of Neuroscience, Norwegian University of Science and Technology, Trondheim, Norway
| | - Timothy Lynch
- 11 Dublin Neurological Institute at the Mater Misericordiae University Hospital, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - George D Mellick
- 12 Eskitis Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia
| | - Megha Mohan
- 12 Eskitis Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia
| | - Peter A Silburn
- 12 Eskitis Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia.,13 University of Queensland, Asia-Pacific Centre for Neuromodulation, Centre for Clinical Research, Brisbane, Queensland, Australia
| | | | - Carles Vilariño-Güell
- 3 Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA.,15 Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Matthew J Farrer
- 3 Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA.,15 Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Li Chen
- 16 Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,17 Solomon H Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,18 Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130-2685, USA
| | - Valina L Dawson
- 16 Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,17 Solomon H Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,18 Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130-2685, USA.,19 Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,20 Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ted M Dawson
- 16 Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,17 Solomon H Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,18 Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130-2685, USA.,19 Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,21 Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Owen A Ross
- 3 Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA.,23 School of Medicine and Medical Science, University College Dublin, Dublin, Ireland.,24 Mayo Graduate School, Neurobiology of Disease, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Wolfdieter Springer
- 3 Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA .,24 Mayo Graduate School, Neurobiology of Disease, Mayo Clinic, Jacksonville, FL 32224, USA
| |
Collapse
|
134
|
Ahmad S, Ytterberg AJ, Thulasingam M, Tholander F, Bergman T, Zubarev R, Wetterholm A, Rinaldo-Matthis A, Haeggström JZ. Phosphorylation of Leukotriene C4 Synthase at Serine 36 Impairs Catalytic Activity. J Biol Chem 2016; 291:18410-8. [PMID: 27365393 DOI: 10.1074/jbc.m116.735647] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Indexed: 01/07/2023] Open
Abstract
Leukotriene C4 synthase (LTC4S) catalyzes the formation of the proinflammatory lipid mediator leukotriene C4 (LTC4). LTC4 is the parent molecule of the cysteinyl leukotrienes, which are recognized for their pathogenic role in asthma and allergic diseases. Cellular LTC4S activity is suppressed by PKC-mediated phosphorylation, and recently a downstream p70S6k was shown to play an important role in this process. Here, we identified Ser(36) as the major p70S6k phosphorylation site, along with a low frequency site at Thr(40), using an in vitro phosphorylation assay combined with mass spectrometry. The functional consequences of p70S6k phosphorylation were tested with the phosphomimetic mutant S36E, which displayed only about 20% (20 μmol/min/mg) of the activity of WT enzyme (95 μmol/min/mg), whereas the enzyme activity of T40E was not significantly affected. The enzyme activity of S36E increased linearly with increasing LTA4 concentrations during the steady-state kinetics analysis, indicating poor lipid substrate binding. The Ser(36) is located in a loop region close to the entrance of the proposed substrate binding pocket. Comparative molecular dynamics indicated that Ser(36) upon phosphorylation will pull the first luminal loop of LTC4S toward the neighboring subunit of the functional homotrimer, thereby forming hydrogen bonds with Arg(104) in the adjacent subunit. Because Arg(104) is a key catalytic residue responsible for stabilization of the glutathione thiolate anion, this phosphorylation-induced interaction leads to a reduction of the catalytic activity. In addition, the positional shift of the loop and its interaction with the neighboring subunit affect active site access. Thus, our mutational and kinetic data, together with molecular simulations, suggest that phosphorylation of Ser(36) inhibits the catalytic function of LTC4S by interference with the catalytic machinery.
Collapse
Affiliation(s)
| | - A Jimmy Ytterberg
- Chemistry I, and Department of Medicine, Solna, Karolinska Institutet, SE-171 76 Stockholm, Sweden
| | | | - Fredrik Tholander
- Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden and
| | | | | | | | | | | |
Collapse
|
135
|
Bietz S, Fährrolfes R, Rarey M. The Art of Compiling Protein Binding Site Ensembles. Mol Inform 2016; 35:593-598. [PMID: 27870245 DOI: 10.1002/minf.201600043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 04/25/2016] [Indexed: 01/24/2023]
Abstract
Structure-based drug design starts with the collection, preparation, and initial analysis of protein structures. With more than 115,000 structures publically available in the Protein Data Bank (PDB), fully automated processes reliably performing these important preprocessing steps are needed. Several tools are available for these tasks, however, most of them do not address the special needs of scientists interested in protein-ligand interactions. In this paper, we summarize our research activities towards an automated processing pipeline from raw PDB data towards ready-to-use protein binding site ensembles. Starting from a single protein structure, the pipeline covers the following phases: Extracting structurally related binding sites from the PDB, aligning disconnected binding site sequences, resolving tautomeric forms and protonation, orienting hydrogens and flippable side-chains, structurally aligning the multitude of binding sites, and performing a reasonable reduction of ensemble structures. The pipeline, named SIENA, creates protein-structural ensembles for the analysis of protein flexibility, molecular design efforts like docking or de novo design within seconds. For the first time, we are able to process the whole PDB in order to create a large collection of protein binding site ensembles. SIENA is available as part of the ZBH ProteinsPlus webserver under http://proteinsplus.zbh.uni-hamburg.de.
Collapse
Affiliation(s)
- Stefan Bietz
- University of Hamburg, ZBH -, Center for Bioinformatics, Bundesstraße 43, 20146, Hamburg, Germany
| | - Rainer Fährrolfes
- University of Hamburg, ZBH -, Center for Bioinformatics, Bundesstraße 43, 20146, Hamburg, Germany
| | - Matthias Rarey
- University of Hamburg, ZBH -, Center for Bioinformatics, Bundesstraße 43, 20146, Hamburg, Germany
| |
Collapse
|
136
|
Culbertson AT, Tietze AA, Tietze D, Chou YH, Smith AL, Young ZT, Zabotina OA. A homology model of Xyloglucan Xylosyltransferase 2 reveals critical amino acids involved in substrate binding. Glycobiology 2016; 26:961-972. [DOI: 10.1093/glycob/cww050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 04/14/2016] [Indexed: 11/14/2022] Open
|
137
|
Borbulevych O, Martin RI, Tickle IJ, Westerhoff LM. XModeScore: a novel method for accurate protonation/tautomer-state determination using quantum-mechanically driven macromolecular X-ray crystallographic refinement. Acta Crystallogr D Struct Biol 2016; 72:586-98. [PMID: 27050137 PMCID: PMC4822566 DOI: 10.1107/s2059798316002837] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 02/17/2016] [Indexed: 11/16/2022] Open
Abstract
Gaining an understanding of the protein-ligand complex structure along with the proper protonation and explicit solvent effects can be important in obtaining meaningful results in structure-guided drug discovery and structure-based drug discovery. Unfortunately, protonation and tautomerism are difficult to establish with conventional methods because of difficulties in the experimental detection of H atoms owing to the well known limitations of X-ray crystallography. In the present work, it is demonstrated that semiempirical, quantum-mechanics-based macromolecular crystallographic refinement is sensitive to the choice of a protonation-state/tautomer form of ligands and residues, and can therefore be used to explore potential states. A novel scoring method, called XModeScore, is described which enumerates the possible protomeric/tautomeric modes, refines each mode against X-ray diffraction data with the semiempirical quantum-mechanics (PM6) Hamiltonian and scores each mode using a combination of energetic strain (or ligand strain) and rigorous statistical analysis of the difference electron-density distribution. It is shown that using XModeScore it is possible to consistently distinguish the correct bound protomeric/tautomeric modes based on routine X-ray data, even at lower resolutions of around 3 Å. These X-ray results are compared with the results obtained from much more expensive and laborious neutron diffraction studies for three different examples: tautomerism in the acetazolamide ligand of human carbonic anhydrase II (PDB entries 3hs4 and 4k0s), tautomerism in the 8HX ligand of urate oxidase (PDB entries 4n9s and 4n9m) and the protonation states of the catalytic aspartic acid found within the active site of an aspartic protease (PDB entry 2jjj). In each case, XModeScore applied to the X-ray diffraction data is able to determine the correct protonation state as defined by the neutron diffraction data. The impact of QM-based refinement versus conventional refinement on XModeScore is also discussed.
Collapse
Affiliation(s)
- Oleg Borbulevych
- QuantumBio Inc., 2790 West College Avenue, State College, PA 16801, USA
| | - Roger I. Martin
- QuantumBio Inc., 2790 West College Avenue, State College, PA 16801, USA
| | - Ian J. Tickle
- Astex Pharmaceuticals, 436 Science Park, Milton Road, Cambridge CB4 0QA, England
| | | |
Collapse
|
138
|
Improved Homology Model of the Human all-trans Retinoic Acid Metabolizing Enzyme CYP26A1. Molecules 2016; 21:351. [PMID: 26999080 PMCID: PMC6274249 DOI: 10.3390/molecules21030351] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 03/07/2016] [Accepted: 03/09/2016] [Indexed: 11/17/2022] Open
Abstract
A new CYP26A1 homology model was built based on the crystal structure of cyanobacterial CYP120A1. The model quality was examined for stereochemical accuracy, folding reliability, and absolute quality using a variety of different bioinformatics tools. Furthermore, the docking capabilities of the model were assessed by docking of the natural substrate all-trans-retinoic acid (atRA), and a group of known azole- and tetralone-based CYP26A1 inhibitors. The preferred binding pose of atRA suggests the (4S)-OH-atRA metabolite production, in agreement with recently available experimental data. The distances between the ligands and the heme group iron of the enzyme are in agreement with corresponding distances obtained for substrates and azole inhibitors for other cytochrome systems. The calculated theoretical binding energies agree with recently reported experimental data and show that the model is capable of discriminating between natural substrate, strong inhibitors (R116010 and R115866), and weak inhibitors (liarozole, fluconazole, tetralone derivatives).
Collapse
|
139
|
Sane S, Abdullah A, Nelson ME, Wang H, Chauhan SC, Newton SS, Rezvani K. Structural studies of UBXN2A and mortalin interaction and the putative role of silenced UBXN2A in preventing response to chemotherapy. Cell Stress Chaperones 2016; 21:313-26. [PMID: 26634371 PMCID: PMC4786526 DOI: 10.1007/s12192-015-0661-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 11/16/2015] [Accepted: 11/18/2015] [Indexed: 12/26/2022] Open
Abstract
Overexpression of the oncoprotein mortalin in cancer cells and its protein partners enables mortalin to promote multiple oncogenic signaling pathways and effectively antagonize chemotherapy-induced cell death. A UBX-domain-containing protein, UBXN2A, acts as a potential mortalin inhibitor. This current study determines whether UBXN2A effectively binds to and occupies mortalin's binding pocket, resulting in a direct improvement in the tumor's sensitivity to chemotherapy. Molecular modeling of human mortalin's binding pocket and its binding to the SEP domain of UBXN2A followed by yeast two-hybrid and His-tag pull-down assays revealed that three amino acids (PRO442, ILE558, and LYS555) within the substrate-binding domain of mortalin are crucial for UBXN2A binding to mortalin. As revealed by chase experiments in the presence of cycloheximide, overexpression of UBXN2A seems to interfere with the mortalin-CHIP E3 ubiquitin ligase and consequently suppresses the C-terminus of the HSC70-interacting protein (CHIP)-mediated destabilization of p53, resulting in its stabilization in the cytoplasm and upregulation in the nucleus. Overexpression of UBXN2A causes a significant inhibition of cell proliferation and the migration of colon cancer cells. We silenced UBXN2A in the human osteosarcoma U2OS cell line, an enriched mortalin cancer cell, followed by a clinical dosage of the chemotherapeutic agent 5-fluorouracil (5-FU). The UBXN2A knockout U2OS cells revealed that UBXNA is essential for the cytotoxic effect achieved by 5-FU. UBXN2A overexpression markedly increased the apoptotic response of U2OS cells to the 5-FU. In addition, silencing of UBXN2A protein suppresses apoptosis enhanced by UBXN2A overexpression in U2OS. The knowledge gained from this study provides insights into the mechanistic role of UBXN2A as a potent mortalin inhibitor and as a potential chemotherapy sensitizer for clinical application.
Collapse
Affiliation(s)
- Sanam Sane
- Division of Basic Biomedical Sciences, Sanford School of Medicine, The University of South Dakota, 414 E. Clark Street, Lee Medical Building, Vermillion, SD, 57069, USA
| | - Ammara Abdullah
- Division of Basic Biomedical Sciences, Sanford School of Medicine, The University of South Dakota, 414 E. Clark Street, Lee Medical Building, Vermillion, SD, 57069, USA
| | - Morgan E Nelson
- Division of Basic Biomedical Sciences, Sanford School of Medicine, The University of South Dakota, 414 E. Clark Street, Lee Medical Building, Vermillion, SD, 57069, USA
| | - Hongmin Wang
- Division of Basic Biomedical Sciences, Sanford School of Medicine, The University of South Dakota, 414 E. Clark Street, Lee Medical Building, Vermillion, SD, 57069, USA
| | - Subhash C Chauhan
- Department of Pharmaceutical Sciences and Center for Cancer Research, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Samuel S Newton
- Division of Basic Biomedical Sciences, Sanford School of Medicine, The University of South Dakota, 414 E. Clark Street, Lee Medical Building, Vermillion, SD, 57069, USA
| | - Khosrow Rezvani
- Division of Basic Biomedical Sciences, Sanford School of Medicine, The University of South Dakota, 414 E. Clark Street, Lee Medical Building, Vermillion, SD, 57069, USA.
| |
Collapse
|
140
|
Scala A, Micale N, Piperno A, Rescifina A, Schirmeister T, Kesselring J, Grassi G. Targeting of the Leishmania mexicana cysteine protease CPB2.8ΔCTE by decorated fused benzo[b]thiophene scaffold. RSC Adv 2016. [DOI: 10.1039/c6ra05557e] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
A potent and highly selective anhydride-based inhibitor ofLeishmania mexicanacysteine protease CPB2.8 (IC50= 3.7 μM) was investigated by inhibition assays, NMR biomimetic experiments and docking studies.
Collapse
Affiliation(s)
- A. Scala
- Dipartimento di Scienze Chimiche
- Biologiche
- Farmaceutiche ed Ambientali
- Università di Messina
- 98166 Messina
| | - N. Micale
- Dipartimento di Scienze Chimiche
- Biologiche
- Farmaceutiche ed Ambientali
- Università di Messina
- 98166 Messina
| | - A. Piperno
- Dipartimento di Scienze Chimiche
- Biologiche
- Farmaceutiche ed Ambientali
- Università di Messina
- 98166 Messina
| | - A. Rescifina
- Dipartimento di Scienze del Farmaco
- Università degli Studi di Catania
- 95125 Catania
- Italy
| | - T. Schirmeister
- Institute of Pharmacy and Biochemistry
- University of Mainz
- D 55099 Mainz
- Germany
| | - J. Kesselring
- Institute of Pharmacy and Biochemistry
- University of Mainz
- D 55099 Mainz
- Germany
| | - G. Grassi
- Dipartimento di Scienze Chimiche
- Biologiche
- Farmaceutiche ed Ambientali
- Università di Messina
- 98166 Messina
| |
Collapse
|
141
|
Bocola M, Schwaneberg U, Jaeger KE, Krauss U. Light-induced structural changes in a short light, oxygen, voltage (LOV) protein revealed by molecular dynamics simulations-implications for the understanding of LOV photoactivation. Front Mol Biosci 2015; 2:55. [PMID: 26484348 PMCID: PMC4589677 DOI: 10.3389/fmolb.2015.00055] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 09/05/2015] [Indexed: 02/06/2023] Open
Abstract
The modularity of light, oxygen, voltage (LOV) blue-light photoreceptors has recently been exploited for the design of LOV-based optogenetic tools, which allow the light-dependent control of biological functions. For the understanding of LOV sensory function and hence the optimal design of LOV-based optogentic tools it is essential to gain an in depth atomic-level understanding of the underlying photoactivation and intramolecular signal-relay mechanisms. To address this question we performed molecular dynamics simulations on both the dark- and light-adapted state of PpSB1-LOV, a short dimeric bacterial LOV-photoreceptor protein, recently crystallized under constant illumination. While LOV dimers remained globally stable during the light-state simulation with regard to the Jα coiled-coil, distinct conformational changes for a glutamine in the vicinity of the FMN chromophore are observed. In contrast, multiple Jα-helix conformations are sampled in the dark-state. These changes coincide with a displacement of the Iβ and Hβ strands relative to the light-state structure and result in a correlated rotation of both LOV core domains in the dimer. These global changes are most likely initiated by the reorientation of the conserved glutamine Q116, whose side chain flips between the Aβ (dark state) and Hβ strand (light state), while maintaining two potential hydrogen bonds to FMN-N5 and FMN-O4, respectively. This local Q116-FMN reorientation impacts on an inter-subunit salt-bridge (K117-E96), which is stabilized in the light state, hence accounting for the observed decreased mobility. Based on these findings we propose an alternative mechanism for dimeric LOV photoactivation and intramolecular signal-relay, assigning a distinct structural role for the conserved “flipping” glutamine. The proposed mechanism is discussed in light of universal applicability and its implications for the understanding of LOV-based optogenetic tools.
Collapse
Affiliation(s)
- Marco Bocola
- Lehrstuhl für Biotechnologie, RWTH Aachen University Aachen, Germany
| | | | - Karl-Erich Jaeger
- Forschungszentrum Jülich, Institut für Molekulare Enzymtechnologie, Heinrich Heine University Düsseldorf Jülich, Germany ; Forschungszentrum Jülich, Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie Jülich, Germany
| | - Ulrich Krauss
- Forschungszentrum Jülich, Institut für Molekulare Enzymtechnologie, Heinrich Heine University Düsseldorf Jülich, Germany
| |
Collapse
|
142
|
Abdullatypov AV, Tsygankov AA. Modeling three-dimensional structure of two closely related Ni-Fe hydrogenases. PHOTOSYNTHESIS RESEARCH 2015; 125:341-353. [PMID: 25572109 DOI: 10.1007/s11120-014-0071-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 12/15/2014] [Indexed: 06/04/2023]
Abstract
The results of homology modeling of HydSL, a NiFe-hydrogenase from purple sulfur bacterium Thiocapsa roseopersicina BBS, and deep-water bacterium Alteromonas macleodii deep ecotype are presented in this work. It is shown that the models have larger confidence level than earlier published ones; full-size models of these enzymes are presented for the first time. The C-end fragment of small subunit of T. roseopersicina hydrogenase is shown to have random orientation in relation to the main protein globule. The obtained models of this enzyme have a large number of ion pairs, as well as thermostable HydSL hydrogenase from Allochromatium vinosum, in contrast to thermostable HydSL hydrogenase from Alt. macleodii and thermolabile HydAB hydrogenase from Desulfovibrio vulgaris. The possible determinant of oxygen stability of studied hydrogenases could be the lack of several intramolecular tunnels. Hydrophobic and electrostatic surfaces were mapped in order to find out possible pathways of coupling hydrogenase to electron-transferring chains, as well as methods for construction of artificial photobiohydrogen-producing systems.
Collapse
Affiliation(s)
- A V Abdullatypov
- Institute of Basic Biological Problems RAS, Institutskaya, 2, Pushchino, 142290, Moscow Region, Russia,
| | | |
Collapse
|
143
|
Crona M, Hofer A, Astorga-Wells J, Sjöberg BM, Tholander F. Biochemical Characterization of the Split Class II Ribonucleotide Reductase from Pseudomonas aeruginosa. PLoS One 2015. [PMID: 26225432 PMCID: PMC4520616 DOI: 10.1371/journal.pone.0134293] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The opportunistic pathogen Pseudomonas aeruginosa can grow under both aerobic and anaerobic conditions. Its flexibility with respect to oxygen load is reflected by the fact that its genome encodes all three existing classes of ribonucleotides reductase (RNR): the oxygen-dependent class I RNR, the oxygen-indifferent class II RNR, and the oxygen-sensitive class III RNR. The P. aeruginosa class II RNR is expressed as two separate polypeptides (NrdJa and NrdJb), a unique example of a split RNR enzyme in a free-living organism. A split class II RNR is also found in a few closely related γ-Proteobacteria. We have characterized the P. aeruginosa class II RNR and show that both subunits are required for formation of a biologically functional enzyme that can sustain vitamin B12-dependent growth. Binding of the B12 coenzyme as well as substrate and allosteric effectors resides in the NrdJa subunit, whereas the NrdJb subunit mediates efficient reductive dithiol exchange during catalysis. A combination of activity assays and activity-independent methods like surface plasmon resonance and gas phase electrophoretic macromolecule analysis suggests that the enzymatically active form of the enzyme is a (NrdJa-NrdJb)2 homodimer of heterodimers, and a combination of hydrogen-deuterium exchange experiments and molecular modeling suggests a plausible region in NrdJa that interacts with NrdJb. Our detailed characterization of the split NrdJ from P. aeruginosa provides insight into the biochemical function of a unique enzyme known to have central roles in biofilm formation and anaerobic growth.
Collapse
Affiliation(s)
- Mikael Crona
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles väg 2, SE-17177, Stockholm, Sweden
| | - Anders Hofer
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-90187, Umeå, Sweden
| | - Juan Astorga-Wells
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles väg 2, SE-17177, Stockholm, Sweden
| | - Britt-Marie Sjöberg
- Department of Biochemistry and Biophysics, Stockholm University, SE-10691, Stockholm, Sweden
| | - Fredrik Tholander
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles väg 2, SE-17177, Stockholm, Sweden
- * E-mail:
| |
Collapse
|
144
|
Fiesel FC, Ando M, Hudec R, Hill AR, Castanedes-Casey M, Caulfield TR, Moussaud-Lamodière EL, Stankowski JN, Bauer PO, Lorenzo-Betancor O, Ferrer I, Arbelo JM, Siuda J, Chen L, Dawson VL, Dawson TM, Wszolek ZK, Ross OA, Dickson DW, Springer W. (Patho-)physiological relevance of PINK1-dependent ubiquitin phosphorylation. EMBO Rep 2015; 16:1114-30. [PMID: 26162776 DOI: 10.15252/embr.201540514] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 06/25/2015] [Indexed: 11/09/2022] Open
Abstract
Mutations in PINK1 and PARKIN cause recessive, early-onset Parkinson's disease (PD). Together, these two proteins orchestrate a protective mitophagic response that ensures the safe disposal of damaged mitochondria. The kinase PINK1 phosphorylates ubiquitin (Ub) at the conserved residue S65, in addition to modifying the E3 ubiquitin ligase Parkin. The structural and functional consequences of Ub phosphorylation (pS65-Ub) have already been suggested from in vitro experiments, but its (patho-)physiological significance remains unknown. We have generated novel antibodies and assessed pS65-Ub signals in vitro and in cells, including primary neurons, under endogenous conditions. pS65-Ub is dependent on PINK1 kinase activity as confirmed in patient fibroblasts and postmortem brain samples harboring pathogenic mutations. We show that pS65-Ub is reversible and barely detectable under basal conditions, but rapidly induced upon mitochondrial stress in cells and amplified in the presence of functional Parkin. pS65-Ub accumulates in human brain during aging and disease in the form of cytoplasmic granules that partially overlap with mitochondrial, lysosomal, and total Ub markers. Additional studies are now warranted to further elucidate pS65-Ub functions and fully explore its potential for biomarker or therapeutic development.
Collapse
Affiliation(s)
| | - Maya Ando
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Roman Hudec
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | | | | | | | | | - Peter O Bauer
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Isidre Ferrer
- Institut de Neuropatologia, Servei d'Anatomia Patològica Hospital Universitari de Bellvitge, Hospitalet del Llobregat, Spain CIBERNED, Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, Instituto de Salud Carlos III, Barcelona, Spain
| | - José M Arbelo
- Department of Neurology, Parkinson's and Movement Disorders Unit, Hospital Universitario Insular de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Joanna Siuda
- Department of Neurology, School of Medicine in Katowice Medical University of Silesia, Katowice, Poland
| | - Li Chen
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering Johns Hopkins University School of Medicine, Baltimore, MD, USA Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering Johns Hopkins University School of Medicine, Baltimore, MD, USA Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, USA Diana Helis Henry Medical Research Foundation, New Orleans, LA, USA
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering Johns Hopkins University School of Medicine, Baltimore, MD, USA Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, USA Diana Helis Henry Medical Research Foundation, New Orleans, LA, USA Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Owen A Ross
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA Neurobiology of Disease, Mayo Graduate School, Jacksonville, FL, USA
| | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA Neurobiology of Disease, Mayo Graduate School, Jacksonville, FL, USA
| | - Wolfdieter Springer
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA Neurobiology of Disease, Mayo Graduate School, Jacksonville, FL, USA
| |
Collapse
|
145
|
Fiesel FC, Caulfield TR, Moussaud-Lamodière EL, Ogaki K, Dourado DFAR, Flores SC, Ross OA, Springer W. Structural and Functional Impact of Parkinson Disease-Associated Mutations in the E3 Ubiquitin Ligase Parkin. Hum Mutat 2015; 36:774-86. [PMID: 25939424 DOI: 10.1002/humu.22808] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 04/23/2015] [Indexed: 12/24/2022]
Abstract
Mutations in the PARKIN/PARK2 gene that result in loss-of-function of the encoded, neuroprotective E3 ubiquitin ligase Parkin cause recessive, familial early-onset Parkinson disease. As an increasing number of rare Parkin sequence variants with unclear pathogenicity are identified, structure-function analyses will be critical to determine their disease relevance. Depending on the specific amino acids affected, several distinct pathomechanisms can result in loss of Parkin function. These include disruption of overall Parkin folding, decreased solubility, and protein aggregation. However pathogenic effects can also result from misregulation of Parkin autoinhibition and of its enzymatic functions. In addition, interference of binding to coenzymes, substrates, and adaptor proteins can affect its catalytic activity too. Herein, we have performed a comprehensive structural and functional analysis of 21 PARK2 missense mutations distributed across the individual protein domains. Using this combined approach, we were able to pinpoint some of the pathogenic mechanisms of individual sequence variants. Similar analyses will be critical in gaining a complete understanding of the complex regulations and enzymatic functions of Parkin. These studies will not only highlight the important residues, but will also help to develop novel therapeutics aimed at activating and preserving an active, neuroprotective form of Parkin.
Collapse
Affiliation(s)
| | | | | | - Kotaro Ogaki
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida
| | - Daniel F A R Dourado
- Department of Cell & Molecular Biology, Computational & Systems Biology, Uppsala University, Uppsala, Sweden
| | - Samuel C Flores
- Department of Cell & Molecular Biology, Computational & Systems Biology, Uppsala University, Uppsala, Sweden
| | - Owen A Ross
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida.,Mayo Graduate School, Neurobiology of Disease, Mayo Clinic, Jacksonville, Florida
| | - Wolfdieter Springer
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida.,Mayo Graduate School, Neurobiology of Disease, Mayo Clinic, Jacksonville, Florida
| |
Collapse
|
146
|
Computational docking simulations of a DNA-aptamer for argininamide and related ligands. J Comput Aided Mol Des 2015; 29:643-54. [PMID: 25877490 DOI: 10.1007/s10822-015-9844-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 04/09/2015] [Indexed: 10/23/2022]
Abstract
The binding properties of sequence-specific nucleic acids (aptamers) to low-molecular-weight ligands, macromolecules and even cells attract substantial scientific interest. These ligand-DNA complexes found different applications for sensing, nanomedicine, and DNA nanotechnology. Structural information on the aptamer-ligand complexes is, however, scarce, even though it would open-up the possibilities to design novel features in the complexes. In the present study we apply molecular docking simulations to probe the features of an experimentally documented L-argininamide aptamer complex. The docking simulations were performed using AutoDock 4.0 and YASARA Structure software, a well-suited program for following intermolecular interactions and structures of biomolecules, including DNA. We explored the binding features of a DNA aptamer to L-argininamide and to a series of arginine derivatives or arginine-like ligands. We find that the best docking results are obtained after an energy-minimization of the parent ligand-aptamer complexes. The calculated binding energies of all mono-substituted guanidine-containing ligands show a good correlation with the experimentally determined binding constants. The results provide valuable guidelines for the application of docking simulations for the prediction of aptamer-ligand structures, and for the design of novel features of ligand-aptamer complexes.
Collapse
|
147
|
Culbertson JE, Chung DH, Ziebart KT, Espiritu E, Toney MD. Conversion of aminodeoxychorismate synthase into anthranilate synthase with Janus mutations: mechanism of pyruvate elimination catalyzed by chorismate enzymes. Biochemistry 2015; 54:2372-84. [PMID: 25710100 DOI: 10.1021/acs.biochem.5b00013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The central importance of chorismate enzymes in bacteria, fungi, parasites, and plants combined with their absence in mammals makes them attractive targets for antimicrobials and herbicides. Two of these enzymes, anthranilate synthase (AS) and aminodeoxychorismate synthase (ADCS), are structurally and mechanistically similar. The first catalytic step, amination at C2, is common between them, but AS additionally catalyzes pyruvate elimination, aromatizing the aminated intermediate to anthranilate. Despite prior attempts, the conversion of a pyruvate elimination-deficient enzyme into an elimination-proficient one has not been reported. Janus, a bioinformatics method for predicting mutations required to functionally interconvert homologous enzymes, was employed to predict mutations to convert ADCS into AS. A genetic selection on a library of Janus-predicted mutations was performed. Complementation of an AS-deficient strain of Escherichia coli grown on minimal medium led to several ADCS mutants that allow growth in 6 days compared to 2 days for wild-type AS. The purified mutant enzymes catalyze the conversion of chorismate to anthranilate at rates that are ∼50% of the rate of wild-type ADCS-catalyzed conversion of chorismate to aminodeoxychorismate. The residues mutated do not contact the substrate. Molecular dynamics studies suggest that pyruvate elimination is controlled by the conformation of the C2-aminated intermediate. Enzymes that catalyze elimination favor the equatorial conformation, which presents the C2-H to a conserved active site lysine (Lys424) for deprotonation and maximizes stereoelectronic activation. Acid/base catalysis of pyruvate elimination was confirmed in AS and salicylate synthase by showing incorporation of a solvent-derived proton into the pyruvate methyl group and by solvent kinetic isotope effects on pyruvate elimination catalyzed by AS.
Collapse
Affiliation(s)
- Justin E Culbertson
- †Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Dong hee Chung
- †Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Kristin T Ziebart
- ‡Department of Chemistry, Oregon State University, Corvallis, Oregon 97331-4003, United States
| | - Eduardo Espiritu
- §Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Michael D Toney
- †Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| |
Collapse
|
148
|
Elbadawi MAA, Awadalla MKA, Hamid MMA, Mohamed MA, Awad TA. Valproic acid as a potential inhibitor of Plasmodium falciparum histone deacetylase 1 (PfHDAC1): an in silico approach. Int J Mol Sci 2015; 16:3915-31. [PMID: 25679451 PMCID: PMC4346934 DOI: 10.3390/ijms16023915] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 01/30/2015] [Indexed: 11/25/2022] Open
Abstract
A new Plasmodium falciparum histone deacetylase1 (PfHDAC1) homology model was built based on the highest sequence identity available template human histone deacetylase 2 structure. The generated model was carefully evaluated for stereochemical accuracy, folding correctness and overall structure quality. All evaluations were acceptable and consistent. Docking a group of hydroxamic acid histone deacetylase inhibitors and valproic acid has shown binding poses that agree well with inhibitor-bound histone deacetylase-solved structural interactions. Docking affinity dG scores were in agreement with available experimental binding affinities. Further, enzyme-ligand complex stability and reliability were investigated by running 5-nanosecond molecular dynamics simulations. Thorough analysis of the simulation trajectories has shown that enzyme-ligand complexes were stable during the simulation period. Interestingly, the calculated theoretical binding energies of the docked hydroxamic acid inhibitors have shown that the model can discriminate between strong and weaker inhibitors and agrees well with the experimental affinities reported in the literature. The model and the docking methodology can be used in screening virtual libraries for PfHDAC1 inhibitors, since the docking scores have ranked ligands in accordance with experimental binding affinities. Valproic acid calculated theoretical binding energy suggests that it may inhibit PfHDAC1.
Collapse
Affiliation(s)
| | | | - Muzamil Mahdi Abdel Hamid
- Department of Parasitology and Medical Entomology, Institute of Endemic Diseases, University of Khartoum, Khartoum 11111, Sudan.
| | - Magdi Awadalla Mohamed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Khartoum, Khartoum 11111, Sudan.
| | - Talal Ahmed Awad
- Medicinal and Aromatic Plants Research Institute, National Centre of Research, Khartoum 11111, Sudan.
| |
Collapse
|
149
|
Rescifina A, Scala A, Sciortino MT, Colao I, Siracusano G, Mazzaglia A, Chiacchio U, Grassi G. Decorated 6,6′,7,7′-tetrahydro-1H,1′H-2,3′-biindole scaffold as promising candidate for recognition of the CDK2 allosteric site. MEDCHEMCOMM 2015. [DOI: 10.1039/c4md00364k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Decorated 6,6′,7,7′-tetrahydro-1H,1′H-2,3′-biindoles, such as DPIT, targeting CDK2 seem to be an attractive scaffold for development of useful anticancer drugs.
Collapse
Affiliation(s)
- Antonio Rescifina
- Dipartimento di Scienze del Farmaco
- Università di Catania
- 95125 Catania
- Italy
| | - Angela Scala
- Dipartimento di Scienze Chimiche
- Università di Messina
- 98166 Messina
- Italy
| | | | - Ivana Colao
- Dipartimento di Scienze Biologiche ed Ambientali
- Università di Messina
- 98166 Messina
- Italy
| | - Gabriel Siracusano
- Dipartimento di Scienze Biologiche ed Ambientali
- Università di Messina
- 98166 Messina
- Italy
| | - Antonino Mazzaglia
- CNR-ISMN Istituto per lo Studio dei Materiali Nanostrutturati c/o Dipartimento di Scienze Chimiche dell'Università di Messina
- 98166 Messina
- Italy
| | - Ugo Chiacchio
- Dipartimento di Scienze del Farmaco
- Università di Catania
- 95125 Catania
- Italy
| | - Giovanni Grassi
- Dipartimento di Scienze Chimiche
- Università di Messina
- 98166 Messina
- Italy
| |
Collapse
|
150
|
Taylor JL, Price JE, Toney MD. Directed evolution of the substrate specificity of dialkylglycine decarboxylase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1854:146-55. [PMID: 25500286 DOI: 10.1016/j.bbapap.2014.12.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 11/19/2014] [Accepted: 12/03/2014] [Indexed: 11/19/2022]
Abstract
Dialkylglycine decarboxylase (DGD) is an unusual pyridoxal phosphate dependent enzyme that catalyzes decarboxylation in the first and transamination in the second half-reaction of its ping-pong catalytic cycle. Directed evolution was employed to alter the substrate specificity of DGD from 2-aminoisobutyrate (AIB) to 1-aminocyclohexane-1-carboxylate (AC6C). Four rounds of directed evolution led to the identification of several mutants, with clones in the final rounds containing five persistent mutations. The best clones show ~2.5-fold decrease in KM and ~2-fold increase in kcat, giving a modest ~5-fold increase in catalytic efficiency for AC6C. Additional rounds of directed evolution did not improve catalytic activity toward AC6C. Only one (S306F) of the five persistent mutations is close to the active site. S306F was observed in all 33 clones except one, and the mutation is shown to stabilize the enzyme toward denaturation. The other four persistent mutations are near the surface of the enzyme. The S306F mutation and the distal mutations all have significant effects on the kinetic parameters for AIB and AC6C. Molecular dynamics simulations suggest that the mutations alter the conformational landscape of the enzyme, favoring a more open active site conformation that facilitates the reactivity of the larger substrate. We speculate that the small increases in kcat/KM for AC6C are due to two constraints. The first is the mechanistic requirement for catalyzing oxidative decarboxylation via a concerted decarboxylation/proton transfer transition state. The second is that DGD must catalyze transamination at the same active site in the second half-reaction of the ping-pong catalytic cycle.
Collapse
Affiliation(s)
- Jared L Taylor
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - Joseph E Price
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - Michael D Toney
- Department of Chemistry, University of California, Davis, CA 95616, USA.
| |
Collapse
|