ABSTRACT
BACKGROUND: The molecular dynamics is an approach to obtain kinetic and thermodynamic characteristics of biomolecular structures. The molecular dynamics simulation softwares are very useful, however, most of them are used in command line form and continue with the same common implementation difficulties that plague researchers who are not computer specialists. RESULTS: Here, we have developed the VisualDynamics-a WEB tool developed to automate biological simulations performed in Gromacs using a graphical interface to make molecular dynamics simulation user-friendly task. In this new application the researcher can submit a simulation of the protein in the free form or complexed with a ligand. Can also download the graphics analysis and log files at the end of the simulation. CONCLUSIONS: VisualDynamics is a tool that will accelerate implementations and learning in the area of molecular dynamics simulation. Freely available at https://visualdynamics.fiocruz.br/login , is supported by all major web browsers. VisualDynamics was developed with Flask, which is a Python-based free and open-source framework for web development. The code is freely available for download at GitHub https://github.com/LABIOQUIM/visualdynamics .
Subject(s)
Molecular Dynamics Simulation , Software , Proteins/chemistry , Kinetics , Web BrowserABSTRACT
The neurohormone oxytocin is a key player in the modulation of reproductive and social behavioral traits, such as parental care. Recently, a correlation between different forms of oxytocin and behavioral phenotypes has been described in the New World Monkeys (NWMs). Here, we demonstrate that, compared with the Leu8OXT found in most placental mammals, the Cebidae Pro8OXT and Saguinus Val3Pro8OXT taxon-specific variants act as equi-efficacious agonists for the Gq-dependent pathway but are weaker agonists for the ß-arrestin engagement and subsequent endocytosis toward the oxytocin receptor (OXTR). Upon interaction with the AVPR1a, Pro8OXT and the common Leu8OXT yielded similar signaling profiles, being equally efficacious on Gq and ß-arrestin, while Val3Pro8OXT showed reduced relative efficacy toward ß-arrestin. Intranasal treatment with either of the variants increased maternal behavior and also promoted unusual paternal care in rats, as measured by pup-retrieval tests. We therefore suggest that Val3Pro8OXT and Pro8OXT are functional variants, which might have been evolutionarily co-opted as an essential part of the adaptive genetic repertoire that allowed the emergence of taxon-specific complex social behaviors, such as intense parental care in the Cebidae and the genus Saguinus.
Subject(s)
Behavior, Animal/drug effects , Maternal Behavior/drug effects , Oxytocin/pharmacology , Paternal Behavior/drug effects , Administration, Intranasal , Animals , Animals, Newborn , Female , Genetic Variation , HEK293 Cells , Humans , Male , Oxytocin/administration & dosage , Oxytocin/genetics , Platyrrhini , Rats , Receptors, Oxytocin/agonists , Receptors, Oxytocin/genetics , Receptors, Oxytocin/metabolism , Signal Transduction/drug effects , Signal Transduction/geneticsABSTRACT
Anthracyclines, e.g., doxorubicin (DOX), and anthracenediones, e.g., mitoxantrone (MTX), are drugs used in the chemotherapy of several cancer types, including solid and non-solid malignancies such as breast cancer, leukemia, lymphomas, and sarcomas. Although they are effective in tumor therapy, treatment with these two drugs may lead to side effects such as arrhythmia and heart failure. At the same clinically equivalent dose, MTX causes slightly reduced cardiotoxicity compared with DOX. These drugs interact with iron to generate reactive oxygen species (ROS), target topoisomerase 2 (Top2), and impair mitochondria. These are some of the mechanisms through which these drugs induce late cardiomyopathy. In this review, we compare the cardiotoxicities of these two chemotherapeutic drugs, DOX and MTX. As described here, even though they share similarities in their modes of toxicant action, DOX and MTX seem to differ in a key aspect. DOX is a more redox-interfering drug, while MTX induces energy imbalance. In addition, DOX toxicity can be explained by underlying mechanisms that include targeting of Top2 beta, mitochondrial impairment, and increases in ROS generation. These modes of action have not yet been demonstrated for MTX, and this knowledge gap needs to be filled.
Subject(s)
Antibiotics, Antineoplastic/toxicity , Doxorubicin/toxicity , Heart Diseases/chemically induced , Mitoxantrone/toxicity , Myocytes, Cardiac/drug effects , Signal Transduction/drug effects , Animals , Antigens, Neoplasm/metabolism , Cardiotoxicity , DNA Topoisomerases, Type II/metabolism , DNA-Binding Proteins/metabolism , Heart Diseases/metabolism , Heart Diseases/pathology , Heart Diseases/prevention & control , Humans , Iron/metabolism , Mitochondria, Heart/drug effects , Mitochondria, Heart/metabolism , Mitochondria, Heart/pathology , Myocytes, Cardiac/metabolism , Myocytes, Cardiac/pathology , Oxidation-Reduction , Oxidative Stress/drug effects , Poly-ADP-Ribose Binding Proteins , Reactive Oxygen Species/metabolism , Topoisomerase II Inhibitors/pharmacologyABSTRACT
Due to the high rate of transmissibility, Brazil became the new COVID-19 outbreak epicenter and, since then, is being monitored to understand how SARS-CoV-2 mutates and spreads. We combined genomic and structural analysis to evaluate genomes isolated from different regions of Brazil and show that the most prevalent mutations were located in the S, N, ORF3a and ORF6 genes, which are involved in different stages of viral life cycle and its interaction with the host cells. Structural analysis brought to light the positions of these mutations on protein structures, contributing towards studies of selective structure-based drug discovery and vaccine development.
Subject(s)
COVID-19/genetics , Mutation/genetics , SARS-CoV-2/genetics , Viral Proteins/genetics , Brazil , Genome, Viral , Genomics , Humans , SARS-CoV-2/pathogenicity , Severity of Illness IndexABSTRACT
In humans, purine nucleoside phosphorylase (HsPNP) is responsible for degradation of deoxyguanosine, and genetic deficiency of this enzyme leads to profound T-cell mediated immunosuppression. HsPNP is a target for inhibitor development aiming at T-cell immune response modulation. Here we report the crystal structure of HsPNP in complex with 7-deazaguanine (HsPNP:7DG) at 2.75 A. Molecular dynamics simulations were employed to assess the structural features of HsPNP in both free form and in complex with 7DG. Our results show that some regions, responsible for entrance and exit of substrate, present a conformational variability, which is dissected by dynamics simulation analysis. Enzymatic assays were also carried out and revealed that 7-deazaguanine presents a lower inhibitory activity against HsPNP (K(i)=200 microM). The present structure may be employed in both structure-based design of PNP inhibitors and in development of specific empirical scoring functions.
Subject(s)
Guanine/analogs & derivatives , Molecular Dynamics Simulation , Purine-Nucleoside Phosphorylase/chemistry , Purine-Nucleoside Phosphorylase/metabolism , X-Ray Diffraction/methods , Guanine/chemistry , Guanine/metabolism , Humans , Molecular Structure , Principal Component Analysis , Protein Binding , Protein Structure, Secondary , Protein Structure, Tertiary , Spectrometry, FluorescenceABSTRACT
Although molecular dynamics encompasses several applications, studies focusing on biomolecular systems are central issues of this research area. Such simulations require the generation of trajectory files, which provide a path for the analysis and interpretation of results with biological significance. However, although several programs have been developed in Python language for the analyses of molecular dynamics (MD) trajectories, they usually require some knowledge of programming languages in order to write or run the scripts using command lines, which certainly hinders the access of MD simulations to many scientists with the necessary biological background to interpret their results. To ease the access to Python packages focusing on MD trajectory analyses, we built a user-friendly and easy-to-install graphical PyMOL interface. Geo-Measures integrates the PyMOL functionalities with MDTraj, a powerful library of trajectory analyses, allowing the users to access up to 14 different types of analyses. Two sample cases are reported here to demonstrate the use of Geo-Measures. In the first example, which involves the use a MD trajectory file of hemoglobin from the MoDEL MD bank, we exemplified the analyses of the following variables: root mean square deviation, radius of gyration, free energy landscape and principal component analysis. In the second case, we built a trajectory file for the ecto-5'-nucleotidase using the LiGRO program to study the carbon alpha pincer angles, to define the secondary structure of the proteins and to analyze the Modevectors. This user-friendly graphical PyMOL plugin, which can be used to generate several descriptive analyses for protein structures, is open source and can be downloaded at: https://pymolwiki.org/index.php/Geo_Measures_Plugin.
ABSTRACT
Tuberculosis (TB) is one of the most common infectious diseases known to man and responsible for millions of human deaths in the world. The increasing incidence of TB in developing countries, the proliferation of multidrug resistant strains, and the absence of resources for treatment have highlighted the need of developing new drugs against TB. The shikimate pathway leads to the biosynthesis of chorismate, a precursor of aromatic amino acids. This pathway is absent from mammals and shown to be essential for the survival of Mycobacterium tuberculosis, the causative agent of TB. Accordingly, enzymes of aromatic amino acid biosynthesis pathway represent promising targets for structure-based drug design. The first reaction in phenylalanine biosynthesis involves the conversion of chorismate to prephenate, catalyzed by chorismate mutase. The second reaction is catalyzed by prephenate dehydratase (PDT) and involves decarboxylation and dehydratation of prephenate to form phenylpyruvate, the precursor of phenylalanine. Here, we describe utilization of different techniques to infer the structure of M. tuberculosis PDT (MtbPDT) in solution. Small angle X-ray scattering and ultracentrifugation analysis showed that the protein oligomeric state is a tetramer and MtbPDT is a flat disk protein. Bioinformatics tools were used to infer the structure of MtbPDT. A molecular model for MtbPDT is presented and molecular dynamics simulations indicate that MtbPDT is stable. Experimental and molecular modeling results were in agreement and provide evidence for a tetrameric state of MtbPDT in solution.
Subject(s)
Computer Simulation , Models, Molecular , Mycobacterium tuberculosis/enzymology , Prephenate Dehydratase/chemistry , Protein Structure, Secondary , Recombinant Proteins/chemistry , Scattering, Small Angle , Ultracentrifugation , X-Ray DiffractionABSTRACT
Human purine nucleoside phosphorylase (HsPNP) is a target for inhibitor development aiming at T-cell immune response modulation. In this work, we report the development of a new set of empirical scoring functions and its application to evaluate binding affinities and docking results. To test these new functions, we solved the structure of HsPNP and 2-mercapto-4(3H)-quinazolinone (HsPNP:MQU) binary complex at 2.7A resolution using synchrotron radiation, and used these functions to predict ligand position obtained in docking simulations. We also employed molecular dynamics simulations to analyze HsPNP in two conditions, as apoenzyme and in the binary complex form, in order to assess the structural features responsible for stability. Analysis of the structural differences between systems provides explanation for inhibitor binding. The use of these scoring functions to evaluate binding affinities and molecular docking results may be used to guide future efforts on virtual screening focused on HsPNP.
Subject(s)
Apoenzymes/chemistry , Purine-Nucleoside Phosphorylase/chemistry , Purine-Nucleoside Phosphorylase/metabolism , Quinazolinones/metabolism , Binding Sites , Computer Simulation , Enzyme Stability , Humans , Kinetics , Ligands , Models, Molecular , Molecular Structure , Protein Binding , Protein Conformation , Protein Structure, Secondary , Purine-Nucleoside Phosphorylase/genetics , Quinazolinones/chemistry , Recombinant Proteins/chemistry , Recombinant Proteins/isolation & purification , Recombinant Proteins/metabolism , Reproducibility of Results , Spectrometry, Fluorescence , Structure-Activity Relationship , Synchrotrons , Titrimetry , X-Ray DiffractionABSTRACT
Bacillus anthracis has been used as weapon in bioterrorist activities, with high mortality, despite anti-microbial treatment, which strongly indicates a need of new drugs to treat anthrax. Shikimate Pathway is a seven-step biosynthetic route which generates chorismic acid. The shikimate pathway is essential for many pathological organisms, whereas it is absent in mammals. Therefore, these enzymes are potential targets for the development of non-toxic anti-microbial agents and herbicides and have been submitted to intensive structural studies. Shikimate Kinase is the fifth enzyme of shikimate pathway and catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimate using ATP as a co-substrate, resulting in shikimate-3-phosphate and ADP. The present work describes for the first time a structural model for the Shikimate Kinase from B. anthracis using molecular modeling approach and molecular dynamics simulations. This study was able to identify the main residues of the ATP-binding and the shikimate pockets responsible for ligand affinities. Analysis of the molecular dynamics simulations indicates the structural features responsible for the stability of the structure. This study may help in the identification of new inhibitors for this enzyme.
Subject(s)
Bacillus anthracis/enzymology , Computer Simulation , Models, Chemical , Phosphotransferases (Alcohol Group Acceptor)/chemistry , Binding Sites , Ligands , Models, Molecular , Time FactorsABSTRACT
This work describes for the first time a structural model of purine nucleoside phosphorylase from Streptococcus agalactiae (SaPNP). PNP catalyzes the cleavage of N-ribosidic bonds of the purine ribonucleosides and 2-deoxyribonucleosides in the presence of inorganic orthophosphate as a second substrate. This enzyme is a potential target for the development of antibacterial drugs. We modeled the complexes of SaPNP with 15 different ligands in order to determine the structural basis for the specificity of these ligands against SaPNP. The application of a novel empirical scoring function to estimate the affinity of a ligand for a protein was able to identify the ligands with high affinity for PNPs. The analysis of molecular dynamics trajectory for SaPNP indicates that the functionally important motifs have a very stable structure. This new structural model together with a novel empirical scoring function opens the possibility to explorer larger library of compounds in order to identify the new inhibitors for PNPs in virtual screening projects.
Subject(s)
Computer Simulation , Purine-Nucleoside Phosphorylase/chemistry , Streptococcus agalactiae/enzymology , Amino Acid Sequence , Binding Sites , Catalysis , Deoxyribonucleosides/chemistry , Guanosine/analogs & derivatives , Guanosine/pharmacology , Humans , Hydrogen Bonding , Inosine/analogs & derivatives , Inosine/pharmacology , Ligands , Models, Molecular , Molecular Sequence Data , Purine Nucleosides/chemistry , Purine-Nucleoside Phosphorylase/antagonists & inhibitors , Sequence Alignment , Structure-Activity Relationship , Time FactorsABSTRACT
The family of Cyclin-Dependent Kinases (CDKs) can be subdivided into two major functional groups based on their roles in cell cycle and/or transcriptional control. CDK9 is the catalytic subunit of positive transcription elongation factor b (P-TEFb). CDK9 is the kinase of the TAK complex (Tat-associated kinase complex), and binds to Tat protein of HIV, suggesting a possible role for CDK9 in AIDS progression. CDK9 complexed with its regulatory partner cyclin T1, serves as a cellular mediator of the transactivation function of the HIV Tat protein. P-TEFb is responsible for the phosphorylation of the carboxyl-terminal domain of RNA Pol II, resulting in stimulation of transcription. Furthermore, the complexes containing CDK9 induce the differentiation in distinct tissue. The CDK9/cyclin T1 complex is expressed at higher level in more differentiated primary neuroectodermal and neuroblastoma tumors, showing a correlation between the kinase expression and tumor differentiation grade. This may have clinical and therapeutical implications for these tumor types. Among the CDK inhibitors two have shown to be effective against CDK9: Roscovitine and Flavopiridol. These two inhibitors prevented the replication of human immunodeficiency virus (HIV) type 1 by blocking Tat transactivation of the HIV type 1 promoter. These compounds inhibit CDKs by binding to the catalytic domain in place of ATP, preventing transfer of a phosphate group to the substrate. More sensitive therapeutic agents of CDK9 can be designed, and structural studies can add information in the understanding of this kinase. The major features related to CDK9 inhibition will be reviewed in this article.
Subject(s)
Cyclin-Dependent Kinase 9/antagonists & inhibitors , Cyclin-Dependent Kinase 9/chemistry , Amino Acid Sequence , Catalytic Domain , Cloning, Molecular , Cyclin-Dependent Kinase 9/physiology , Flavones/chemistry , Flavones/pharmacology , Humans , Models, Molecular , Molecular Sequence Data , Purines/chemistry , Purines/pharmacology , Pyrazoles/chemistry , Pyrazoles/pharmacology , Recombinant Proteins/antagonists & inhibitors , Recombinant Proteins/chemistry , Recombinant Proteins/isolation & purification , Sequence AlignmentABSTRACT
The PI3K/Akt/mTOR pathway is an important intracellular signaling pathway in cell cycle regulation and its dysregulation is associated with various types of diseases. mTOR (mechanistic or mammalian target of rapamycin) is the main enzyme that performs intermediate control of the signaling pathway through a phosphotransfer process. The classical inhibition of the mTOR pathway is effected by rapamycin and its analogous blocking allosterically the catalytic phosphorylation site, avoiding the deleterious side effects induced by ATP-competitive inhibitors. We employed ligand-based drug design strategies such as pharmacophore searching and analysis, molecular docking, absorption, distribution, metabolism, excretion and toxicity (ADMETox) properties filtering, and molecular dynamics to select potential molecules to become non-ATP competitive inhibitors of the mTOR complex. According to our findings, we propose eight novel potential mTOR inhibitors with similar or better properties than the classic inhibitor complex, rapamycin.
Subject(s)
Molecular Docking Simulation , Molecular Dynamics Simulation , Protein Kinase Inhibitors/chemistry , TOR Serine-Threonine Kinases/chemistry , Binding Sites , Drug Design , Humans , Ligands , Molecular Conformation , Protein Binding , Protein Kinase Inhibitors/pharmacology , Quantitative Structure-Activity Relationship , Reproducibility of Results , TOR Serine-Threonine Kinases/antagonists & inhibitorsABSTRACT
The mTOR (mammalian or mechanistic Target Of Rapamycin), a complex metabolic pathway that involves multiple steps and regulators, is a major human metabolic pathway responsible for cell growth control in response to multiple factors and that is dysregulated in various types of cancer. The classical inhibition of the mTOR pathway is performed by rapamycin and its analogs (rapalogs). Considering that rapamycin binds to an allosteric site and performs a crucial role in the inhibition of the mTOR complex without causing the deleterious side effects common to ATP-competitive inhibitors, we employ ligand-based drug design strategies, such as virtual screening methodology, computational determination of ADME/Tox properties of selected molecules, and molecular dynamics in order to select molecules with the potential to become non-ATP-competitive inhibitors of the mTOR enzymatic complex. Our findings suggest five novel potential mTOR inhibitors, with similar or better properties than the classic inhibitor complex, rapamycin.
Subject(s)
Adenosine Triphosphate/chemistry , Antibiotics, Antineoplastic/chemistry , Protein Kinase Inhibitors/chemistry , Sirolimus/chemistry , TOR Serine-Threonine Kinases/chemistry , Allosteric Site , Drug Design , Humans , Kinetics , Ligands , Molecular Docking Simulation , Molecular Dynamics Simulation , Protein Binding , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Protein Interaction Domains and Motifs , Structure-Activity Relationship , Substrate Specificity , TOR Serine-Threonine Kinases/antagonists & inhibitors , Thermodynamics , User-Computer InterfaceABSTRACT
To speed up the drug-discovery process, molecular dynamics (MD) calculations performed in GROMACS can be coupled to docking simulations for the post-screening analyses of large compound libraries. This requires generating the topology of the ligands in different software, some basic knowledge of Linux command lines, and a certain familiarity in handling the output files. LiGRO-the python-based graphical interface introduced here-was designed to overcome these protein-ligand parameterization challenges by allowing the graphical (non command line-based) control of GROMACS (MD and analysis), ACPYPE (ligand topology builder) and PLIP (protein-binder interactions monitor)-programs that can be used together to fully perform and analyze the outputs of complex MD simulations (including energy minimization and NVT/NPT equilibration). By allowing the calculation of linear interaction energies in a simple and quick fashion, LiGRO can be used in the drug-discovery pipeline to select compounds with a better protein-binding interaction profile. The design of LiGRO allows researchers to freely download and modify the software, with the source code being available under the terms of a GPLv3 license from http://www.ufrgs.br/lasomfarmacia/ligro/ .
Subject(s)
Drug Discovery/methods , Ligands , Molecular Dynamics Simulation , Proteins/chemistry , Software , Computational Biology/methods , Protein Binding , Proteins/metabolism , User-Computer InterfaceABSTRACT
BACKGROUND: Tuberculosis (TB) still remains one of the most deadly infectious diseases in the world. Mycobacterium tuberculosis ß-ketoacyl-ACP Reductase (MabA) is a member of the fatty acid elongation system type II, providing precursors of mycolic acids that are essential to the bacterial cell growth and survival. MabA has been shown to be essential for M. tuberculosis survival and to play a role in intracellular signal transduction of bacilli. FINDINGS: Here we describe site-directed mutagenesis, recombinant protein expression and purification, steady-state kinetics, fluorescence spectroscopy, and molecular modeling for S140T and S140A mutant MabA enzymes. No enzyme activity could be detected for S140T and S140A. Although the S140T protein showed impaired NADPH binding, the S140A mutant could bind to NADPH. Computational predictions for NADPH binding affinity to WT, S140T and S140A MabA proteins were consistent with fluorescence spectroscopy data. CONCLUSIONS: The results suggest that the main role of the S140 side chain of MabA is in catalysis. The S140 side chain appears to also play an indirect role in NADPH binding. Interestingly, NADPH titrations curves shifted from sigmoidal for WT to hyperbolic for S140A, suggesting that the S140 residue may play a role in displacing the pre-existing equilibrium between two forms of MabA in solution. The results here reported provide a better understanding of the mode of action of MabA that should be useful to guide the rational (function-based) design of inhibitors of MabA enzyme activity which, hopefully, could be used as lead compounds with anti-TB action.
Subject(s)
Alcohol Oxidoreductases/metabolism , Bacterial Proteins/metabolism , Mycobacterium tuberculosis/enzymology , Serine/metabolism , 3-Oxoacyl-(Acyl-Carrier-Protein) Reductase , Alcohol Oxidoreductases/chemistry , Alcohol Oxidoreductases/genetics , Amino Acid Substitution , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Binding Sites/genetics , Humans , Hydrogen Bonding , Kinetics , Models, Molecular , Mutagenesis, Site-Directed , Mutation , Mycobacterium tuberculosis/genetics , NADP/chemistry , NADP/metabolism , Protein Binding , Protein Structure, Tertiary , Recombinant Proteins/metabolism , Serine/genetics , Spectrometry, Fluorescence , Tuberculosis/microbiologyABSTRACT
Purine nucleoside phosphorylase (PNP) (EC.2.4.2.1) is an enzyme that catalyzes the cleavage of N-ribosidic bonds of the purine ribonucleosides and 2-deoxyribonucleosides in the presence of inorganic orthophosphate as a second substrate. This enzyme is involved in purine-salvage pathway and has been proposed as a promising target for design and development of antimalarial and antibacterial drugs. Recent elucidation of the three-dimensional structure of PNP by X-ray protein crystallography left open the possibility of structure-based virtual screening initiatives in combination with molecular dynamics simulations focused on identification of potential new antimalarial drugs. Most of the previously published molecular dynamics simulations of PNP were carried out on human PNP, a trimeric PNP. The present article describes for the first time molecular dynamics simulations of hexameric PNP from Plasmodium falciparum (PfPNP). Two systems were simulated in the present work, PfPNP in ligand free form, and in complex with immucillin and sulfate. Based on the dynamical behavior of both systems the main results related to structural stability and protein-drug interactions are discussed.
Subject(s)
Molecular Dynamics Simulation , Plasmodium falciparum/enzymology , Protein Multimerization , Purine-Nucleoside Phosphorylase/chemistry , Binding Sites , Biocatalysis , Enzyme Stability , Phosphates/metabolism , Pliability , Protein Structure, Tertiary , Purine Nucleosides/chemistry , Purine Nucleosides/metabolism , Purine-Nucleoside Phosphorylase/metabolism , Pyrimidinones/chemistry , Pyrimidinones/metabolism , Sulfates/metabolism , Time FactorsABSTRACT
Bacillus anthracis has been employed as an agent of bioterrorism, with high mortality, despite anti-microbial treatment, which strongly indicates the need of new drugs to treat anthrax. Shikimate pathway is a seven step biosynthetic route which generates chorismic acid from phosphoenol pyruvate and erythrose-4-phosphate. Chorismic acid is the major branch point in the synthesis of aromatic amino acids, ubiquinone, and secondary metabolites. The shikimate pathway is essential for many pathological organisms, whereas it is absent in mammals. Therefore, these enzymes are potential targets for the development of nontoxic antimicrobial agents and herbicides and have been submitted to intensive structural studies. The forth enzyme of this pathway is responsible for the conversion of dehydroshikimate to shikimate in the presence of NADP. In order to pave the way for structural and functional efforts toward development of new antimicrobials we describe the molecular modeling of shikimate dehydrogenase from Bacillus anthracis complexed with the cofactor NADP. This study was able to identify the main residues of the NADP binding site responsible for ligand affinities. This structural study can be used in the design of more specific drugs against infectious diseases.
Subject(s)
Alcohol Oxidoreductases/chemistry , Bacillus anthracis/enzymology , Models, Molecular , NADP/chemistry , Anti-Bacterial Agents/chemistry , Binding Sites , Drug Design , Protein Conformation , Shikimic Acid/analogs & derivatives , Shikimic Acid/chemistryABSTRACT
Purine nucleoside phosphorylase (PNP) catalyzes the reversible phosphorolysis of N-ribosidic bonds of purine nucleosides and deoxynucleosides, except adenosine, to generate ribose 1-phosphate and the purine base. This work describes for the first time a structural model of PNP from Bacteroides fragilis (Bf). We modeled the complexes of BfPNP with six different ligands in order to determine the structural basis for specificity of these ligands against BfPNP. Comparative analysis of the model of BfPNP and the structure of HsPNP allowed identification of structural features responsible for differences in the computationally determined ligand affinities. The molecular dynamics (MD) simulation was assessed to evaluate the overall stability of the BfPNP model. The superposition of the final onto the initial minimized structure shows that there are no major conformational changes from the initial model, which is consistent with the relatively low root mean square deviation (RMSD). The results indicate that the structure of the model was stable during MD, and does not exhibit loosely structured loop regions or domain terminals.
Subject(s)
Bacterial Proteins/chemistry , Bacteroides fragilis/enzymology , Models, Molecular , Purine-Nucleoside Phosphorylase/chemistry , Algorithms , Amino Acid Sequence , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Bacteroides fragilis/genetics , Binding Sites/genetics , Binding, Competitive , Computer Simulation , Enzyme Stability , Humans , Kinetics , Ligands , Molecular Sequence Data , Molecular Structure , Protein Binding , Protein Structure, Tertiary , Purine-Nucleoside Phosphorylase/genetics , Purine-Nucleoside Phosphorylase/metabolism , Sequence Homology, Amino AcidABSTRACT
Purine Nucleoside Phosphorylase (PNP) catalyzes the reversible phosphorolysis of N-glycosidic bonds of purine nucleosides and deoxynucleosides, except for adenosine, to generate ribose 1-phosphate and the purine base. PNP has been submitted to intensive structural studies. This work describes for the first time a structural model of PNP from Streptococcus pyogenes (SpPNP). We modeled the complexes of SpPNP with six different ligands in order to determine the structural basis for specificity of these ligands against SpPNP. Molecular dynamics (MD) simulations were performed in order to evaluate the overall stability of SpPNP model. The analysis of the MD simulation was assessed mainly by principal component analysis (PCA) to explore the trimeric structure behavior. Structural comparison, between SpPNP and human PNP, was able to identify the main features responsible for differences in ligand-binding affinities, such as mutation in the purine-binding site and in the second phosphate-binding site. The PCA analysis suggests a different behavior for each subunit in the trimer structure.
Subject(s)
Computer Simulation , Models, Molecular , Purine-Nucleoside Phosphorylase/chemistry , Streptococcus pyogenes/enzymology , Amino Acid Sequence , Binding Sites , Humans , Ligands , Molecular Sequence Data , Purine-Nucleoside Phosphorylase/metabolism , Sequence AlignmentABSTRACT
Drug development has become the Holy Grail of many structural bioinformatics groups. The explosion of information about protein structures, ligand-binding affinity, parasite genome projects, and biological activity of millions of molecules opened the possibility to correlate this scattered information in order to generate reliable computational models to predict the likelihood of being able to modulate a target with a small-molecule drug. Computational methods have shown their potential in drug discovery and development allied with in vitro and in vivo methodologies. The present review discusses the main bioinformatics tools available for drug discovery and development.