scholarly journals Frag4Lead: growing crystallographic fragment hits by catalog using fragment-guided template docking

2021 ◽  
Vol 77 (9) ◽  
pp. 1168-1182 ◽  
Author(s):  
Alexander Metz ◽  
Jan Wollenhaupt ◽  
Steffen Glöckner ◽  
Niki Messini ◽  
Simon Huber ◽  
...  
Keyword(s):  
Structural Information ◽  
Binding Pocket ◽  
Titration Calorimetry ◽  
Attractive Alternative ◽  
Single Digit ◽  
X Ray Crystallography ◽  
Fragment Screening ◽  
Full Control ◽  
Docking Calculations

In recent years, crystallographic fragment screening has matured into an almost routine experiment at several modern synchrotron sites. The hits of the screening experiment, i.e. small molecules or fragments binding to the target protein, are revealed along with their 3D structural information. Therefore, they can serve as useful starting points for further structure-based hit-to-lead development. However, the progression of fragment hits to tool compounds or even leads is often hampered by a lack of chemical feasibility. As an attractive alternative, compound analogs that embed the fragment hit structurally may be obtained from commercial catalogs. Here, a workflow is reported based on filtering and assessing such potential follow-up compounds by template docking. This means that the crystallographic binding pose was integrated into the docking calculations as a central starting parameter. Subsequently, the candidates are scored on their interactions within the binding pocket. In an initial proof-of-concept study using five starting fragments known to bind to the aspartic protease endothiapepsin, 28 follow-up compounds were selected using the designed workflow and their binding was assessed by crystallography. Ten of these compounds bound to the active site and five of them showed significantly increased affinity in isothermal titration calorimetry of up to single-digit micromolar affinity. Taken together, this strategy is capable of efficiently evolving the initial fragment hits without major synthesis efforts and with full control by X-ray crystallography.

scholarly journals Mass spectrometry for fragment screening

2017 ◽  
Vol 61 (5) ◽  
pp. 465-473 ◽  
Author(s):  
Daniel Shiu-Hin Chan ◽  
Andrew J. Whitehouse ◽  
Anthony G. Coyne ◽  
Chris Abell
Keyword(s):  
Drug Discovery ◽  
High Sensitivity ◽  
Titration Calorimetry ◽  
Label Free ◽  
X Ray ◽  
X Ray Crystallography ◽  
Fragment Screening ◽  
Differential Scanning Fluorimetry ◽  
Biophysical Techniques

Fragment-based approaches in chemical biology and drug discovery have been widely adopted worldwide in both academia and industry. Fragment hits tend to interact weakly with their targets, necessitating the use of sensitive biophysical techniques to detect their binding. Common fragment screening techniques include differential scanning fluorimetry (DSF) and ligand-observed NMR. Validation and characterization of hits is usually performed using a combination of protein-observed NMR, isothermal titration calorimetry (ITC) and X-ray crystallography. In this context, MS is a relatively underutilized technique in fragment screening for drug discovery. MS-based techniques have the advantage of high sensitivity, low sample consumption and being label-free. This review highlights recent examples of the emerging use of MS-based techniques in fragment screening.

scholarly journals Identification and Optimization of PDE10A Inhibitors Using Fragment-Based Screening by Nanocalorimetry and X-ray Crystallography

2013 ◽  
Vol 19 (4) ◽  
pp. 497-507 ◽  
Author(s):  
Michael I. Recht ◽  
Vandana Sridhar ◽  
John Badger ◽  
Pierre-Yves Bounaud ◽  
Cheyenne Logan ◽  
...  
Keyword(s):  
High Resolution ◽  
Structural Information ◽  
Spectroscopic Properties ◽  
Low Complexity ◽  
Titration Calorimetry ◽  
Label Free ◽  
Lead Discovery ◽  
X Ray ◽  
X Ray Crystallography ◽  
Heavy Atoms

Fragment-based lead discovery (FBLD) is a technique in which small, low-complexity chemical fragments of 6 to 15 heavy atoms are screened for binding to or inhibiting activity of the target. Hits are then linked and/or elaborated into tightly binding ligands, ideally yielding early lead compounds for drug discovery. Calorimetry provides a label-free method to assay binding and enzymatic activity that is unaffected by the spectroscopic properties of the sample. Conventional microcalorimetry is hampered by requiring large quantities of reagents and long measurement times. Nanocalorimeters can overcome these limitations of conventional isothermal titration calorimetry. Here we use enthalpy arrays, which are arrays of nanocalorimeters, to perform an enzyme activity-based fragment screen for competitive inhibitors of phosphodiesterase 10A (PDE10A). Two dozen fragments with KI <2 mM were identified and moved to crystal soaking trials. All soak experiments yielded high-resolution diffraction, with two-thirds of the fragments yielding high-resolution co-crystal structures with PDE10A. The structural information was used to elaborate fragment hits, yielding leads with KI <1 µM. This study shows how array calorimetry can be used as a prescreening method for fragment-based lead discovery with enzyme targets and paired successfully with an X-ray crystallography secondary screen.

Metabolic intervention targeting 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (PFKFB3) using a structure-based design.

2012 ◽  
Vol 30 (15_suppl) ◽  
pp. e13518-e13518
Author(s):  
Lars Ährlund-Richter ◽  
Katarina Färnegårdh ◽  
Elisee Wiita ◽  
Mattias Jönsson ◽  
Carina Norström ◽  
...  
Keyword(s):  
Cell Growth ◽  
High Throughput ◽  
High Throughput Screening ◽  
Structural Information ◽  
Human Cancer ◽  
Isothermal Calorimetry ◽  
Binding Pocket ◽  
Binding Modes ◽  
X Ray ◽  
X Ray Crystallography

e13518 Background: By producing fructose-2,6-bisphosphate, PFKFB3 functions as an activator of anaerobic glycolysis. PFKFB3 is both over expressed and over activated in many of the types of human cancer. Specific inhibition of the PFKFB3 enzyme results in a reduction in metabolism and cell growth in oxygen-deficient cancer environments. Methods: High-throughput screening. Medicinal Chemistry. Structure-Based Drug Design, X-ray Crystallography. NMR. Isothermal Calorimetry. Dynamic Light Scatttering. ADME. Results: A high-throughput screening of 50.000 selected compounds, by means of a biochemical assay, generated 105 hits including both ATP-and non-ATP competitive hits as identified by NMR binding experiments. The latter type was prioritized and two hits with a similar “ring-linker-ring structure” were selected for further expansions. Interestingly, although structurally similar, the two hits were found by means of X-ray crystallography to exhibit different binding modes within the fructose pocket. Based on their respective binding mode, two chemical series were developed displaying different ADME properties and PFKFB isoenzyme selectivity. Calorimetry verified a reversible strong enthalpy driven, direct binding for both chemical series. A third chemical series was developed towards yet another unoccupied binding pocket within the fructose-site, yielding a 5-fold increase in potency. Strong interactions within the new pocket were confirmed using X-ray crystallography. Our PFKFB3 inhibitors were shown to reduce tumor cell growth in vitro and to exhibit combinatory effects with Cisplatin. Conclusions: We have targeted the fructose-binding pocket of PFKFB3, developed compounds with nM binding potency and have gained a detailed understanding of SAR via structural information. The structure-based analysis has provided a good understanding of the molecular interactions, which is important for further biological/clinical positioning: e.g., combination with chemotherapy, optimization of PK properties and proof of principle in vivo.

scholarly journals Elucidation of Molecular Mechanism of a Selective PPARα Modulator, Pemafibrate, through Combinational Approaches of X-ray Crystallography, Thermodynamic Analysis, and First-Principle Calculations

2020 ◽  
Vol 21 (1) ◽  
pp. 361 ◽  
Author(s):  
Mayu Kawasaki ◽  
Akira Kambe ◽  
Yuta Yamamoto ◽  
Sundaram Arulmozhiraja ◽  
Sohei Ito ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Molecular Mechanism ◽  
Structural Changes ◽  
Molecular Level ◽  
Hydrophobic Interactions ◽  
Binding Pocket ◽  
Titration Calorimetry ◽  
X Ray ◽  
X Ray Crystallography ◽  
Steroid Receptor Coactivator

The selective PPARα modulator (SPPARMα) is expected to medicate dyslipidemia with minimizing adverse effects. Recently, pemafibrate was screened from the ligand library as an SPPARMα bearing strong potency. Several clinical pieces of evidence have proved the usefulness of pemafibrate as a medication; however, how pemafibrate works as a SPPARMα at the molecular level is not fully known. In this study, we investigate the molecular mechanism behind its novel SPPARMα character through a combination of approaches of X-ray crystallography, isothermal titration calorimetry (ITC), and fragment molecular orbital (FMO) analysis. ITC measurements have indicated that pemafibrate binds more strongly to PPARα than to PPARγ. The crystal structure of PPARα-ligand binding domain (LBD)/pemafibrate/steroid receptor coactivator-1 peptide (SRC1) determined at 3.2 Å resolution indicates that pemafibrate binds to the ligand binding pocket (LBP) of PPARα in a Y-shaped form. The structure also reveals that the conformation of the phenoxyalkyl group in pemafibrate is flexible in the absence of SRC1 coactivator peptide bound to PPARα; this gives a freedom for the phenoxyalkyl group to adopt structural changes induced by the binding of coactivators. FMO calculations have indicated that the accumulation of hydrophobic interactions provided by the residues at the LBP improve the interaction between pemafibrate and PPARα compared with the interaction between fenofibrate and PPARα.

scholarly journals Achieving a Good Crystal System for Crystallographic X-ray Fragment Screening

2018 ◽  
Author(s):  
Patrick M. Collins ◽  
Alice Douangamath ◽  
Romain Talon ◽  
Alexandre Dias ◽  
José Brandão-Neto ◽  
...  
Keyword(s):  
User Program ◽  
X Ray ◽  
Crystal System ◽  
X Ray Crystallography ◽  
Fragment Screening ◽  
Surface Sites ◽  
Screening Experiment ◽  
Active User ◽  
Density Maps

The XChem facility at Diamond Light Source offers fragment screening by X-ray crystallography as a general access user program. &nbsp;The main advantage of X-ray crystallography as a primary fragment screen is that it yields directly the location and pose of the fragment hits, whether within pockets of interest or merely on surface sites:&nbsp; this is the key information for structure-based design and for enabling synthesis of follow-up molecules. Extensive streamlining of the screening experiment at XChem has engendered a very active user programme that is generating large amounts of data: &nbsp;in 2017, 36 academic and industry groups generated 35,000 datasets of uniquely soaked crystals. &nbsp;It has also generated a large number of learnings concerning the main remaining bottleneck, namely obtaining a suitable crystal system that will support a successful fragment screen.&nbsp; Here we discuss the practicalities of generating screen-ready crystals that have useful electron density maps, and how to ensure they will be successfully reproduced and usable at a facility outside the home lab.

Automated electron tomography: from data collection to image processing

1995 ◽  
Vol 53 ◽  
pp. 26-27
Author(s):  
Weiping Liu ◽  
Jennifer Fung ◽  
W.J. de Ruijter ◽  
Hans Chen ◽  
John W. Sedat ◽  
...  
Keyword(s):  
Image Processing ◽  
Data Collection ◽  
Structural Information ◽  
Imaging Technique ◽  
Electron Tomography ◽  
Ccd Camera ◽  
Automated Data Collection ◽  
Full Control ◽  
Transmission Electron ◽  
Amorphous Structures

Electron tomography is a technique where many projections of an object are collected from the transmission electron microscope (TEM), and are then used to reconstruct the object in its entirety, allowing internal structure to be viewed. As vital as is the 3-D structural information and with no other 3-D imaging technique to compete in its resolution range, electron tomography of amorphous structures has been exercised only sporadically over the last ten years. Its general lack of popularity can be attributed to the tediousness of the entire process starting from the data collection, image processing for reconstruction, and extending to the 3-D image analysis. We have been investing effort to automate all aspects of electron tomography. Our systems of data collection and tomographic image processing will be briefly described.To date, we have developed a second generation automated data collection system based on an SGI workstation (Fig. 1) (The previous version used a micro VAX). The computer takes full control of the microscope operations with its graphical menu driven environment. This is made possible by the direct digital recording of images using the CCD camera.

scholarly journals X-ray crystallography reveals molecular recognition mechanism for sugar binding in a melibiose transporter MelB

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Lan Guan ◽  
Parameswaran Hariharan
Keyword(s):  
Molecular Recognition ◽  
Binding Pocket ◽  
Cation Binding ◽  
Recognition Mechanism ◽  
X Ray ◽  
X Ray Crystallography ◽  
Sugar Binding ◽  
Sugar Specificity ◽  
Major Facilitator ◽  
Mfs Transporters

AbstractMajor facilitator superfamily_2 transporters are widely found from bacteria to mammals. The melibiose transporter MelB, which catalyzes melibiose symport with either Na+, Li+, or H+, is a prototype of the Na+-coupled MFS transporters, but its sugar recognition mechanism has been a long-unsolved puzzle. Two high-resolution X-ray crystal structures of a Salmonella typhimurium MelB mutant with a bound ligand, either nitrophenyl-α-d-galactoside or dodecyl-β-d-melibioside, were refined to a resolution of 3.05 or 3.15 Å, respectively. In the substrate-binding site, the interaction of both galactosyl moieties on the two ligands with MelBSt are virturally same, so the sugar specificity determinant pocket can be recognized, and hence the molecular recognition mechanism for sugar binding in MelB has been deciphered. The conserved cation-binding pocket is also proposed, which directly connects to the sugar specificity pocket. These key structural findings have laid a solid foundation for our understanding of the cooperative binding and symport mechanisms in Na+-coupled MFS transporters, including eukaryotic transporters such as MFSD2A.

Hybrid stenting of the arterial duct with carotid cutdown and flip technique: immediate and early results

2021 ◽  
pp. 1-7
Author(s):  
Supratim Sen ◽  
Priya Pradhan ◽  
Sneha Jain ◽  
Dipesh Trivedi ◽  
Pradeep Kaushik
Keyword(s):  
Interquartile Range ◽  
Attractive Alternative ◽  
Single Centre ◽  
Arterial Access ◽  
Post Procedure ◽  
Arterial Duct ◽  
Early Results ◽  
Carotid Arterial ◽  
Mean Time

Abstract Stenting of the arterial duct (PDA) has become a standard palliation for ductal-dependent pulmonary circulation. Carotid arterial access provides a direct route for stenting vertical ducts. We evaluated our early results of hybrid ductal stenting via surgical carotid cutdown. Methods and results: In this retrospective single centre cohort study, hybrid PDA stenting was attempted in 11 patients with “flip technique”, between January 2020 and February 2021, and was successful in 10. Median age was 29 days (interquartile range 17.5–87) and mean weight 3.37 ± 1.23 kg. Mean fluoroscopy time was 13.58 ± 5.35 minutes, mean procedure time was 48.50 ± 22.5 minutes, and mean radiation dose was 1719.5 ± 1217.6 mGycm2. Mean time for cutdown was 9.9 ± 2.4 minutes and for haemostasis and suturing was 25.3 ± 11.0 minutes. Median duration of ventilation post-stenting was 26 hours (interquartile range 21–43.75). The median ICU stay post-procedure was 5 days (interquartile range 4–7.25) and mean hospital stay was 12 ± 6.3 days. On early follow-up, carotid patency was confirmed in all patients with colour Doppler, with no intravascular thrombi, narrowing, haematomas, or aneurysms noted. There were no complications secondary to vascular access. There was one early mortality, 27 days post-stenting, which was unrelated to the procedure. Conclusion: This study adds to the limited literature on ductal stenting with carotid access and the flip technique. In our early experience, the hybrid carotid approach is an attractive alternative to percutaneous carotid puncture and has simplified a complex and challenging intervention, with good outcomes.

scholarly journals Discovery of Novel Druggable Sites on Zika Virus NS3 Helicase Using X-ray Crystallography-Based Fragment Screening

2018 ◽  
Vol 19 (11) ◽  
pp. 3664 ◽  
Author(s):  
Ali Munawar ◽  
Steven Beelen ◽  
Ahmad Munawar ◽  
Eveline Lescrinier ◽  
Sergei Strelkov
Keyword(s):  
Zika Virus ◽  
Dissociation Constants ◽  
Global Public Health ◽  
Human Pathogens ◽  
Allosteric Site ◽  
Replication Complex ◽  
X Ray ◽  
X Ray Crystallography ◽  
Fragment Screening ◽  
Atomic Precision

The flavivirus family contains several important human pathogens, such as Zika virus (ZIKV), dengue, West Nile, and Yellow Fever viruses, that collectively lead to a large, global disease burden. Currently, there are no approved medicines that can target these viruses. The sudden outbreak of ZIKV infections in 2015–2016 posed a serious threat to global public health. While the epidemic has receded, persistent reservoirs of ZIKV infection can cause reemergence. Here, we have used X-ray crystallography-based screening to discover two novel sites on ZIKV NS3 helicase that can bind drug-like fragments. Both sites are structurally conserved in other flaviviruses, and mechanistically significant. The binding poses of four fragments, two for each of the binding sites, were characterized at atomic precision. Site A is a surface pocket on the NS3 helicase that is vital to its interaction with NS5 polymerase and formation of the flaviviral replication complex. Site B corresponds to a flexible, yet highly conserved, allosteric site at the intersection of the three NS3 helicase domains. Saturation transfer difference nuclear magnetic resonance (NMR) experiments were additionally used to evaluate the binding strength of the fragments, revealing dissociation constants (KD) in the lower mM range. We conclude that the NS3 helicase of flaviviruses is a viable drug target. The data obtained open opportunities towards structure-based design of first-in-class anti-ZIKV compounds, as well as pan-flaviviral therapeutics.

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