Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 20 de 44
Filter
1.
Article in English | MEDLINE | ID: mdl-38806984

ABSTRACT

Sunscreens are essential in protecting the skin from harmful effects of ultraviolet radiation (UVR). These formulations, designed to absorb, block, or scatter UVR, offer vital protection against skin aging, sunburns, and the development of skin cancers like melanomas. However, some sunscreens, especially those containing organic/chemical compounds, can cause allergic reactions. To address this, researchers are extensively investigating formulations that incorporate plant extracts rich in polyphenols, such as flavonoids and carotenoids, which can be considered safer alternatives. Products derived from plants are commonly used in cosmetics to counteract skin aging due to their antioxidant activity that combat harmful free radicals. This review focuses on evaluating the advancements in chemical and natural sunscreens, exploring the integration of polyphenolic nanocarriers within sunscreen formulas, their interaction with UVR, and utilizing nanotechnology to enhance their effectiveness. An attempt has been made to highlight the concerns related to toxicity associated with their use and notable advancements in the regulatory aspects governing their utilization.

2.
J Med Chem ; 67(6): 4541-4559, 2024 Mar 28.
Article in English | MEDLINE | ID: mdl-38466661

ABSTRACT

The optimization of an allosteric fragment, discovered by differential scanning fluorimetry, to an in vivo MAT2a tool inhibitor is discussed. The structure-based drug discovery approach, aided by relative binding free energy calculations, resulted in AZ'9567 (21), a potent inhibitor in vitro with excellent preclinical pharmacokinetic properties. This tool showed a selective antiproliferative effect on methylthioadenosine phosphorylase (MTAP) KO cells, both in vitro and in vivo, providing further evidence to support the utility of MAT2a inhibitors as potential anticancer therapies for MTAP-deficient tumors.


Subject(s)
Neoplasms , Humans , Entropy , Methionine Adenosyltransferase/metabolism
3.
Methods Enzymol ; 690: 85-108, 2023.
Article in English | MEDLINE | ID: mdl-37858541

ABSTRACT

Most drug target interactions for clinically approved small-molecules are non-equilibrium slow-onset, tight-binding or irreversible in nature, with pronounced element of time-dependence of inhibition. Analysis of such modality of inhibition requires a continuous enzyme kinetic measurement that can yield complete progress curves and an automated high-throughput analysis pipeline. Given the increasing emphasis on designing non-equilibrium modes of inhibiting an enzyme target (especially irreversible), the above specified pipeline for data generation and analysis is essential for extracting parameters to guide decisions in early drug discovery. In this manuscript, the methodology and data analysis protocol from our irreversible inhibitor characterization campaigns for the ErbB receptor family members is presented. Guidance is provided on the appropriate design of assay to generate quality data, setting up the analysis and estimation of inactivation rate (kinact) and the pseudo-equilibrium binding affinity (KI) constant (or their ratio kinact/KI) in a high-throughput manner for the inhibitor interacting with the protein target of interest.


Subject(s)
Drug Discovery , ErbB Receptors , ErbB Receptors/metabolism , Kinetics
4.
FEBS J ; 290(23): 5441-5455, 2023 12.
Article in English | MEDLINE | ID: mdl-37014311

ABSTRACT

The ability to view structures of proteins at atomic resolution, facilitated by the rise of macromolecular crystallography, has had a tremendous impact in many areas of sciences, including molecular pharmacology, drug discovery and biotechnology. However, the teaching of macromolecular crystallography in universities across the globe has been less than optimal. This could be attributed to the interdisciplinary nature of this subject, making it appear esoteric and incomprehensible, at least at first glance, for students who have exclusive training in only one specific discipline. For the instructor, this problem is compounded further by the plethora of complex concepts and specialized terminologies that the science of macromolecular crystallography has accumulated over the course of its evolution. Moreover, the advent of robotics and several sophisticated software algorithms have reduced the incentive to understand the beautiful conceptual bedrock on which this subject is based. As a way of addressing some of the challenges delineated above, this Words of Advice article attempts to formulate the broad framework within which the teaching and learning of macromolecular crystallography should be approached. It advocates the acknowledgement that this is an interdisciplinary field, with substantial contributions from chemical, physical, biological and mathematical sciences, requiring the evolution of teaching approaches that acknowledge this reality. Moreover, it suggests the use of visual tools, use of computational resources and history to make the subject more relatable to students.


Subject(s)
Algorithms , Proteins , Humans , Crystallography, X-Ray , Proteins/chemistry , Software , Macromolecular Substances/chemistry
5.
FEBS J ; 290(9): 2292-2305, 2023 05.
Article in English | MEDLINE | ID: mdl-35175693

ABSTRACT

Drugs interact with their target of interest to bring about the desired phenotypic outcome that results in disease alleviation. Traditionally, most lead optimization exercises were driven by affinity measures (like IC50 ) to inform structure-activity relationship (SAR)-guided medicinal chemistry. However, an IC50 value is a thermodynamic estimate measured under equilibrium conditions that can vary as a function of substrate concentration and/or time (the latter especially for nonequilibrium modalities). Further, like other thermodynamic estimates, it is a state-function that is indifferent to the path traversed from the initial state to the final state. This can be a cause for concern in drug discovery given the predominance of nonequilibrium interactions and the open thermodynamic nature of the human system. Under such situations, employing rates along with equilibrium constants (or IC50 values) would be far more relevant to capture the time evolution of the small molecule's interaction with the target of interest. These rates are generally typified by the rate of association, rate of dissociation and the residence time of the small molecule on the target (target occupancy). These parameters, when combined with the concept of target vulnerability, therapeutic window, pharmacokinetic profile of the small molecule, estimates of endogenous ligand and target turnover, will shed critical insights into the kinetics and dynamics of a small molecule's interaction with the protein, and allow realistic modelling of the system to enable optimizations and dosing decisions. With that aim, this guide will attempt to introduce the traditional role of mechanistic enzymology within drug discovery and emphasize the importance of kinetics in guiding SAR-based optimizations. It will also present initial ideas on how kinetic investigation should be positioned relative to the temporal span of a drug-discovery pipeline to leverage maximal utility from the investment in time and effort.


Subject(s)
Physics , Proteins , Humans , Kinetics , Structure-Activity Relationship , Drug Discovery/methods
6.
J Conserv Dent ; 25(4): 356-362, 2022.
Article in English | MEDLINE | ID: mdl-36187864

ABSTRACT

Background: Despite constant advances in science, obscurity remains in the efficient removal of pulp stones to aid in successful root canal treatment. In this context, chemical means of dissolving pulp stones were explored. Aim: The aim of this study is to evaluate and to compare the efficacy of decalcifying agents on the dissolution of pulp stones. Materials and Methods: The study was divided into two groups for pulp stone analysis (21 samples) and dentin analysis (54 samples). Twenty-one pulp stones from patients aged 18-70 who underwent root canal treatment were collected and divided into three subgroups (n = 7) randomly. They were subjected to chemical treatment in a labeled glass container with 5 ml of the respective chemical agents, such as 17% ethylenediaminetetraacetic acid solution (positive control), no treatment (negative control), and newly developed Physiological Simulated Decalcifying Agent (PSDA). At the end of the study period (24 h), the samples were removed, rinsed with deionized water, and subjected to physical analysis, scanning electron microscopy (SEM), and Energy -dispersive X-ray spectroscopy (EDS) analysis. Under dentin analysis, 54 maxillary premolars scheduled for orthodontic extraction without caries or extensive restorations were selected, following which 2-mm thick transverse dentinal sections at the cementoenamel junction level were obtained and randomly divided into two groups for SEM (n = 21) and microhardness analysis (n = 33). The samples were subjected to respective chemical treatment groups similar to pulp stones for 24 h and analyzed using SEM, EDS, and microhardness analysis. Results: Postchemical treatment with the newly developed decalcifying solution, the pulp stones showed the absence of nodular crystallites and surface softening under SEM and a decrease in the calcium level under EDS analysis. Concerning the microhardness of dentin, no significant changes could be observed. Conclusion: The newly explored PSDA was found to be efficacious in the decalcification of pulp stones at a clinically relevant time of 24 h, without significantly affecting the structural integrity and the hardness values of dentin.

7.
SLAS Discov ; 27(8): 460-470, 2022 12.
Article in English | MEDLINE | ID: mdl-36156314

ABSTRACT

Recent efforts for increasing the success in drug discovery focus on an early, massive, and routine mechanistic and/or kinetic characterization of drug-target engagement as part of a design-make-test-analyze strategy. From an experimental perspective, many mechanistic assays can be translated into a scalable format on automation platforms and thereby enable routine characterization of hundreds or thousands of compounds. However, now the limiting factor to achieve such in-depth characterization at high-throughput becomes the quality-driven data analysis, the sheer scale of which outweighs the time available to the scientific staff of most labs. Therefore, automated analytical workflows are needed to enable such experimental scale-up. We have implemented such a fully automated workflow in Genedata Screener for time-dependent ligand-target binding analysis to characterize non-equilibrium inhibitors. The workflow automates Quality Control (QC) / data modelling and decision-making process in a staged analysis: (1) quality control of raw input data-fluorescence signal-based progress curves - featuring automated rejection of unsuitable measurements; (2) automated model selection - one-step versus two-step binding model - using statistical methods and biological validity rules; (3) result visualization in specific plots and annotated result tables, enabling the scientist to review large result sets efficiently and, at the same time, to rapidly identify and focus on interesting or unusual results; (4) an interactive user interface for immediate adjustment of automated decisions, where necessary. Applying this workflow to first-pass, high-throughput kinetic studies on kinase projects has allowed us to surmount previously rate-limiting manual analysis steps and boost productivity; and is now routinely embedded in a biopharma discovery research process.


Subject(s)
Data Analysis , Drug Discovery , Humans , Kinetics
8.
Biochem J ; 479(16): 1727-1741, 2022 08 31.
Article in English | MEDLINE | ID: mdl-35969150

ABSTRACT

DNA/RNA molecules adopting the left-handed conformation (Z-form) have been attributed with immunogenic properties. However, their biological role and importance have been a topic of debate for many years. The discovery of Z-DNA/RNA binding domains (Zα domains) in varied proteins that are involved in the innate immune response, such as the interferon inducible form of the RNA editing enzyme ADAR1 (p150), Z-DNA binding protein 1 (ZBP1), the fish kinase PKZ and the poxvirus inhibitor of interferon response E3L, indicates important roles of Z-DNA/RNA in immunity and self/non-self-discrimination. Such Zα domain-containing proteins recognize left-handed Z-DNA/RNA in a conformation-specific manner. Recent studies have implicated these domains in virus recognition. Given these important emerging roles for the Zα domains, it is pivotal to understand the mechanism of recognition of the Z-DNA/Z-RNA by these domains. To this end, we assessed the binding thermodynamics of Zα domain from ORF112 and ADAR1 on T(CG)3 and T(CG)6 oligonucleotides which have high propensity to adopt the Z-conformation. Our study highlights important differences in the mode of oligonucleotide binding by the two Zα domains originating from different proteins. Site-directed mutagenesis was employed together with isothermal titration calorimetry to tease apart finer details of the binding thermodynamics. Our work advances the understanding on binding thermodynamics of Zα domains to their cognate nucleic acid substrates and paves the ground for future efforts to gain a complete appreciation of this process.


Subject(s)
DNA, Z-Form , Nucleic Acids , Adenosine Deaminase/metabolism , Animals , DNA/metabolism , DNA, Z-Form/genetics , Interferons/genetics , Nucleic Acid Conformation , Oligonucleotides , RNA/metabolism , Thermodynamics
9.
ACS Chem Biol ; 17(8): 2366-2376, 2022 08 19.
Article in English | MEDLINE | ID: mdl-35881961

ABSTRACT

Covalent inhibition is a valuable modality in drug discovery because of its potential ability in decoupling pharmacokinetics from pharmacodynamics by prolonging the residence time of the drug on the target of interest. This increase in target occupancy is limited only by the rate of target turnover. However, a limitation in such studies is to translate the in vitro inhibition assessment to the appropriate in cellulo target engagement parameter by covalent probes. Estimation of such parameters is often impeded by the low-throughput nature of current probe-free approaches. In this study, an ultra-performance liquid chromatography-multiple reaction monitoring mass spectrometry platform was utilized to develop a targeted proteomics workflow that can evaluate cellular on-target engagement of covalent molecules in an increased throughput manner. This workflow enabled a throughput increase of 5-10 fold when compared to traditional nanoLC-based proteomics studies. To demonstrate the applicability of the method, KRASG12C was used as a model system to investigate the interaction of an irreversible covalent small molecule, compound 25, both in vitro and in cellulo. Initial biochemical studies confirmed that the small molecule forms an adduct with the targeted cysteine on the protein, as assessed at the level of both intact protein and on the target peptide. In cellulo studies were carried out to quantify target engagement and allele selectivity assessment for the small molecule in the heterozygous NCI-H358 cell line for KRASG12C with respect to the WT type protein. The workflow enabled evaluation of in vitro and in cellulo target engagement kinetics, providing mechanistic insights into the irreversible mode of inhibition. In summary, the method has the potential for target agnostic application in the assessment of on-target engagement of covalent probes compatible with the high-throughput requirements of early drug discovery.


Subject(s)
Drug Discovery , Proto-Oncogene Proteins p21(ras) , Cysteine , Kinetics , Mutation
10.
FEBS J ; 289(20): 6086-6098, 2022 10.
Article in English | MEDLINE | ID: mdl-34270860

ABSTRACT

The modern definition of enzymology is synonymous with the Michaelis-Menten equation instituted by Leonor Michaelis and Maud Menten. Most textbooks, or chapters within, discussing enzymology start with the derivation of the equation under the assumption of rapid equilibrium (as done by Michaelis-Menten) or steady state (as modified by Briggs and Haldane) conditions to highlight the importance of this equation as the bedrock on which interpretation of enzyme kinetic results is dependent. However, few textbooks or monographs take the effort of placing the equation within its right historical context and discuss the assumptions that have gone into its institution. This guide will dwell on these in substantial detail. Further, this guide will attempt to instil a sense of appreciation for the mathematical curve rectangular hyperbola, its unique attributes and how ubiquitous the curve is in biological systems. To conclude, this guide will discuss the limitations of the equation, and the method it embodies, and trace the journey of how investigators are attempting to move beyond the steady-state approach and the Michaelis-Menten equation into full progress curve, pre-steady state and single-turnover kinetic analysis to obtain greater insights into enzyme kinetics and catalysis.


Subject(s)
Biochemistry , Physics , Catalysis , Enzymes/metabolism , Kinetics , Research Design
11.
J Cell Sci ; 134(10)2021 05 15.
Article in English | MEDLINE | ID: mdl-34037233

ABSTRACT

Zα domains recognize the left-handed helical Z conformation of double-stranded nucleic acids. They are found in proteins involved in the nucleic acid sensory pathway of the vertebrate innate immune system and host evasion by viral pathogens. Previously, it has been demonstrated that ADAR1 (encoded by ADAR in humans) and DAI (also known as ZBP1) localize to cytoplasmic stress granules (SGs), and this localization is mediated by their Zα domains. To investigate the mechanism, we determined the interactions and localization pattern for the N-terminal region of human DAI (ZαßDAI), which harbours two Zα domains, and for a ZαßDAI mutant deficient in nucleic acid binding. Electrophoretic mobility shift assays demonstrated the ability of ZαßDAI to bind to hyperedited nucleic acids, which are enriched in SGs. Furthermore, using immunofluorescence and immunoprecipitation coupled with mass spectrometry, we identified several interacting partners of the ZαßDAI-RNA complex in vivo under conditions of arsenite-induced stress. These interactions are lost upon loss of nucleic acid-binding ability or upon RNase treatment. Thus, we posit that the mechanism for the translocation of Zα domain-containing proteins to SGs is mainly mediated by the nucleic acid-binding ability of their Zα domains. This article has an associated First Person interview with Bharath Srinivasan, joint first author of the paper.


Subject(s)
DNA, Z-Form , Nucleic Acids , Adenosine Deaminase/metabolism , Cytoplasmic Granules/metabolism , Humans , Nucleic Acid Conformation , RNA , RNA-Binding Proteins
12.
SLAS Discov ; 26(5): 684-697, 2021 06.
Article in English | MEDLINE | ID: mdl-33783249

ABSTRACT

Target engagement by small molecules is necessary for producing a physiological outcome. In the past, a lot of emphasis was placed on understanding the thermodynamics of such interactions to guide structure-activity relationships. It is becoming clearer, however, that understanding the kinetics of the interaction between a small-molecule inhibitor and the biological target [structure-kinetic relationship (SKR)] is critical for selection of the optimum candidate drug molecule for clinical trial. However, the acquisition of kinetic data in a high-throughput manner using traditional methods can be labor intensive, limiting the number of molecules that can be tested. As a result, in-depth kinetic studies are often carried out on only a small number of compounds, and usually at a later stage in the drug discovery process. Fundamentally, kinetic data should be used to drive key decisions much earlier in the drug discovery process, but the throughput limitations of traditional methods preclude this. A major limitation that hampers acquisition of high-throughput kinetic data is the technical challenge in collecting substantially confluent data points for accurate parameter estimation from time course analysis. Here, we describe the use of the fluorescent imaging plate reader (FLIPR), a charge-coupled device (CCD) camera technology, as a potential high-throughput tool for generating biochemical kinetic data with smaller time intervals. Subsequent to the design and optimization of the assay, we demonstrate the collection of highly confluent time-course data for various kinase protein targets with reasonable throughput to enable SKR-guided medicinal chemistry. We select kinase target 1 as a special case study with covalent inhibition, and demonstrate methods for rapid and detailed analysis of the resultant kinetic data for parameter estimation. In conclusion, this approach has the potential to enable rapid kinetic studies to be carried out on hundreds of compounds per week and drive project decisions with kinetic data at an early stage in drug discovery.


Subject(s)
Drug Discovery/methods , High-Throughput Screening Assays , Quantitative Structure-Activity Relationship , Drug Discovery/standards , High-Throughput Screening Assays/methods , High-Throughput Screening Assays/standards , Humans , Kinetics , Molecular Imaging/methods , Small Molecule Libraries
13.
ChemMedChem ; 16(6): 899-918, 2021 03 18.
Article in English | MEDLINE | ID: mdl-33231926

ABSTRACT

Biological systems are highly regulated. They are also highly resistant to sudden perturbations enabling them to maintain the dynamic equilibrium essential to sustain life. This robustness is conferred by regulatory mechanisms that influence the activity of enzymes/proteins within their cellular context to adapt to changing environmental conditions. However, the initial rules governing the study of enzyme kinetics were mostly tested and implemented for cytosolic enzyme systems that were easy to isolate and/or recombinantly express. Moreover, these enzymes lacked complex regulatory modalities. Now, with academic labs and pharmaceutical companies turning their attention to more-complex systems (for instance, multiprotein complexes, oligomeric assemblies, membrane proteins and post-translationally modified proteins), the initial axioms defined by Michaelis-Menten (MM) kinetics are rendered inadequate, and the development of a new kind of kinetic analysis to study these systems is required. This review strives to present an overview of enzyme kinetic mechanisms that are atypical and, oftentimes, do not conform to the classical MM kinetics. Further, it presents initial ideas on the design and analysis of experiments in early drug-discovery for such systems, to enable effective screening and characterisation of small-molecule inhibitors with desirable physiological outcomes.


Subject(s)
Drug Discovery , Enzyme Inhibitors/pharmacology , Enzymes/metabolism , Enzyme Inhibitors/chemistry , Humans , Kinetics
14.
FEBS J ; 288(7): 2068-2083, 2021 04.
Article in English | MEDLINE | ID: mdl-32981225

ABSTRACT

Enzymology is concerned with the study of enzyme structure, function, regulation and kinetics. It is an interdisciplinary subject that can be treated as an exclusive sphere of exhaustive inquiry within mathematical, physico-chemical and biological sciences. Hence, teaching of enzymology, in general, and enzyme kinetics, in particular, should be undertaken in an interdisciplinary manner for a holistic appreciation of this subject. Further, analogous examples from everyday life should form an integral component of the teaching for an intuitive grasp of the subject matter. Furthermore, simulation-based appreciation of enzyme kinetics should be preferred over simplifying assumptions and approximations of traditional enzyme kinetics teaching. In this Words of Advice, I outline the domain depth of enzymology across the various disciplines and provide initial ideas on how appropriate analogies can provide firm insights into the subject. Further, I demonstrate how an intuitive feel for the subject can help not only in grasping abstract concepts but also extending it in experimental design and subsequent interpretation. Use of simulations in grasping complex concepts is also advocated given the advantages this medium offers over traditional approaches involving images and molecular models. Furthermore, I discuss the merits of incorporating the historical backdrop of major discoveries in enzymological teaching. We, at AstraZeneca, have experimented with this approach with the desired outcome of generating interest in the subject from people practising diverse disciplines.


Subject(s)
Enzymes/chemistry , Teaching , Enzymes/genetics , Enzymes/ultrastructure , Humans , Kinetics
15.
Eur Endocrinol ; 16(2): 113-121, 2020 Oct.
Article in English | MEDLINE | ID: mdl-33117442

ABSTRACT

Cardiorenal syndrome (CRS) in people with type 2 diabetes mellitus (T2DM) illustrates the bidirectional link between the heart and the kidneys, with acute or chronic dysfunction of one organ adversely impacting the function of the other. Of the five subtypes identified, type 1 and 2 CRS occur because of the adverse impact of cardiac conditions on the kidneys. Type 3 and 4 occur when renal conditions affect the heart, and in type 5, systemic conditions impact the heart and kidneys concurrently. The cardiovascular and renoprotective benefits evidenced with sodium-glucose cotransporter-2 (SGLT2) inhibitors make them a potential choice in the management of CRS. Cardiovascular protection is mediated by a reduction in cardiac workload, blood pressure, and body weight; with improvement in lipid profile, uric acid levels, and adaptive ketogenesis process. Renoprotection is facilitated by reduction in albuminuria and hypoxic stress, and restoration of tubuloglomerular feedback. The favourable effect on cardiovascular complications and death, as well as renal complications and progression to end-stage kidney disease, has been confirmed in clinical trials. Guidelines endorse first-line use of SGLT2 inhibitors after metformin in patients with T2DM with high cardiovascular risk, chronic kidney disease or both. Since most trials with SGLT2 inhibitors excluded subjects with acute illness, patients with CRS subtypes 1 and 3 have not been studied adequately, making SGLT2 initiation in clinical practice challenging. Ongoing trials may provide evidence for SGLT2 inhibitor use in CRS. This review aims to enhance understanding of CRS and provide guidance for judicious use of SGLT2 inhibitors in T2DM.

16.
J Cell Biol ; 219(10)2020 10 05.
Article in English | MEDLINE | ID: mdl-32931551

ABSTRACT

Chromosome segregation during cell division is driven by mitotic spindle attachment to the centromere region on each chromosome. Centromeres form a protein scaffold defined by chromatin featuring CENP-A, a conserved histone H3 variant, in a manner largely independent of local DNA cis elements. CENP-A nucleosomes fulfill two essential criteria to epigenetically identify the centromere. They undergo self-templated duplication to reestablish centromeric chromatin following DNA replication. More importantly, CENP-A incorporated into centromeric chromatin is stably transmitted through consecutive cell division cycles. CENP-A nucleosomes have unique structural properties and binding partners that potentially explain their long lifetime in vivo. However, rather than a static building block, centromeric chromatin is dynamically regulated throughout the cell cycle, indicating that CENP-A stability is also controlled by external factors. We discuss recent insights and identify the outstanding questions on how dynamic control of the long-term stability of CENP-A ensures epigenetic centromere inheritance.


Subject(s)
Centromere Protein A/genetics , Chromosome Segregation/genetics , DNA Replication/genetics , Epigenesis, Genetic/genetics , Autoantigens/genetics , Centromere/genetics , Chromatin/genetics , Chromosomal Proteins, Non-Histone/genetics , DNA-Binding Proteins/genetics , HeLa Cells , Histones/genetics , Humans , Nucleosomes/genetics , Spindle Apparatus/genetics
17.
Nat Commun ; 11(1): 3228, 2020 06 26.
Article in English | MEDLINE | ID: mdl-32591529

ABSTRACT

Plasmodium falciparum (Pf) relies solely on the salvage pathway for its purine nucleotide requirements, making this pathway indispensable to the parasite. Purine nucleotide levels are regulated by anabolic processes and by nucleotidases that hydrolyse these metabolites into nucleosides. Certain apicomplexan parasites, including Pf, have an IMP-specific-nucleotidase 1 (ISN1). Here we show, by comprehensive substrate screening, that PfISN1 catalyzes the dephosphorylation of inosine monophosphate (IMP) and is allosterically activated by ATP. Crystal structures of tetrameric PfISN1 reveal complex rearrangements of domain organization tightly associated with catalysis. Immunofluorescence microscopy and expression of GFP-fused protein indicate cytosolic localization of PfISN1 and expression in asexual and gametocyte stages of the parasite. With earlier evidence on isn1 upregulation in female gametocytes, the structures reported in this study may contribute to initiate the design for possible transmission-blocking agents.


Subject(s)
5'-Nucleotidase/chemistry , 5'-Nucleotidase/metabolism , Biocatalysis , Plasmodium falciparum/enzymology , Adenosine Triphosphate/metabolism , Animals , Apoproteins/metabolism , Binding Sites , Hydrogen-Ion Concentration , Kinetics , Magnesium/metabolism , Mice, Inbred BALB C , Models, Molecular , Mutant Proteins/chemistry , Protein Domains , Protein Structure, Secondary , Protein Transport , Protozoan Proteins/chemistry , Protozoan Proteins/metabolism , Substrate Specificity
18.
Med Res Rev ; 40(5): 1776-1793, 2020 09.
Article in English | MEDLINE | ID: mdl-32285494

ABSTRACT

Understanding protein-small-molecule interactions is a critical component of rational drug-design. Structure-activity relationship (SAR)-guided medicinal chemistry is informed by the biological outcome, as assessed by biochemical activity or cellular effect, of chemical modifications on small molecules. The effectiveness of SAR is reliant on the sturdiness and durability of assay design and the quality of information garnered from assays. Lack of quality data at this step can lead to obstruction of the drug discovery pipeline with profound implications for the timelines of introducing a drug into the market. Hence, it would not be an overstatement to consider biochemical/biological assays as the backbone of drug-discovery. Enzyme assays can fail for many different reasons, with the enzyme and the substrate being the principal players. Lack of clarity can hamper progress and can lead to mounting costs and potentially losing competitive advantage. Although each assay is unique and requires a specific approach to troubleshoot the problem at hand, there are general guidelines that can be followed to maximize the chances of success. This review is a step-by-step attempt at reintroducing fundamental biochemical concepts within the context of an enzyme assay, delineating probable causes for failure and potential approaches to get an assay back up and running.


Subject(s)
Drug Discovery , Enzyme Assays , Biological Assay , Humans , Kinetics , Structure-Activity Relationship
19.
Genome ; 63(2): 61-90, 2020 Feb.
Article in English | MEDLINE | ID: mdl-31557446

ABSTRACT

Nucleobindin-1 is an EF-hand calcium-binding protein with a distinctive profile, predominantly localized to the Golgi in insect and wide-ranging vertebrate cell types, alike. Its putative involvements in intracellular calcium (Ca2+) homeostasis have never been phenotypically characterized in any model organism. We have analyzed an adult-viable mutant that completely disrupts the G protein α-subunit binding and activating (GBA) motif of Drosophila Nucleobindin-1 (dmNUCB1). Such disruption does not manifest any obvious fitness-related, morphological/developmental, or behavioral abnormalities. A single copy of this mutation or the knockdown of dmnucb1 in restricted sets of cells variously rescues pleiotropic mutant phenotypes arising from impaired inositol 1,4,5-trisphosphate receptor (IP3R) activity (in turn depleting cytoplasmic Ca2+ levels across diverse tissue types). Additionally, altered dmNUCB1 expression or function considerably reverses lifespan and mobility improvements effected by IP3R mutants, in a Drosophila model of amyotrophic lateral sclerosis. Homology modeling-based analyses further predict a high degree of conformational conservation in Drosophila, of biochemically validated structural determinants in the GBA motif that specify in vertebrates, the unconventional Ca2+-regulated interaction of NUCB1 with Gαi subunits. The broad implications of our findings are hypothetically discussed, regarding potential roles for NUCB1 in GBA-mediated, Golgi-associated Ca2+ signaling, in health and disease.


Subject(s)
Calcium-Binding Proteins/physiology , Calcium/metabolism , Drosophila Proteins/physiology , Inositol 1,4,5-Trisphosphate Receptors/genetics , Nucleobindins/physiology , Alleles , Amino Acid Motifs , Animals , Calcium-Binding Proteins/chemistry , Calcium-Binding Proteins/genetics , Calcium-Binding Proteins/metabolism , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Drosophila Proteins/chemistry , Drosophila Proteins/genetics , Drosophila Proteins/metabolism , Drosophila melanogaster/genetics , Drosophila melanogaster/growth & development , Drosophila melanogaster/metabolism , GTP-Binding Protein alpha Subunits/metabolism , Genes, Lethal , Genetic Pleiotropy , Golgi Apparatus/metabolism , Homeostasis , Humans , Inositol 1,4,5-Trisphosphate/metabolism , Mutation , Nucleobindins/chemistry , Nucleobindins/genetics , Nucleobindins/metabolism , Protein Domains , Structural Homology, Protein
20.
Med Res Rev ; 39(2): 684-705, 2019 03.
Article in English | MEDLINE | ID: mdl-30192413

ABSTRACT

Escherichia coli Dihydrofolate reductase is an important enzyme that is essential for the survival of the Gram-negative microorganism. Inhibitors designed against this enzyme have demonstrated application as antibiotics. However, either because of poor bioavailability of the small-molecules resulting from their inability to cross the double membrane in Gram-negative bacteria or because the microorganism develops resistance to the antibiotics by mutating the DHFR target, discovery of new antibiotics against the enzyme is mandatory to overcome drug-resistance. This review summarizes the field of DHFR inhibition with special focus on recent efforts to effectively interface computational and experimental efforts to discover novel classes of inhibitors that target allosteric and active-sites in drug-resistant variants of EcDHFR.


Subject(s)
Anti-Bacterial Agents/pharmacology , Bacterial Infections/drug therapy , Enzyme Inhibitors/pharmacology , Escherichia coli/enzymology , Folic Acid Antagonists/pharmacology , Tetrahydrofolate Dehydrogenase/chemistry , Algorithms , Allosteric Site , Animals , Catalytic Domain , Drug Design , Drug Discovery , Humans , Ligands , Permeability/drug effects , Structure-Activity Relationship
SELECTION OF CITATIONS
SEARCH DETAIL
...