scholarly journals Applications of Cryo-EM in small molecule and biologics drug design

2021 ◽  
Author(s):  
Joshua A. Lees ◽  
Joao M. Dias ◽  
Seungil Han
Keyword(s):  
Drug Design ◽  
Structural Characterization ◽  
Viral Vectors ◽  
Biological Macromolecules ◽  
Structure Based Drug Design ◽  
X Ray Crystallography ◽  
Technological Advances ◽  
High Resolution Analysis ◽  
Resolution Analysis

Electron cryo-microscopy (cryo-EM) is a powerful technique for the structural characterization of biological macromolecules, enabling high-resolution analysis of targets once inaccessible to structural interrogation. In recent years, pharmaceutical companies have begun to utilize cryo-EM for structure-based drug design. Structural analysis of integral membrane proteins, which comprise a large proportion of druggable targets and pose particular challenges for X-ray crystallography, by cryo-EM has enabled insights into important drug target families such as G protein-coupled receptors (GPCRs), ion channels, and solute carrier (SLCs) proteins. Structural characterization of biologics, such as vaccines, viral vectors, and gene therapy agents, has also become significantly more tractable. As a result, cryo-EM has begun to make major impacts in bringing critical therapeutics to market. In this review, we discuss recent instructive examples of impacts from cryo-EM in therapeutics design, focusing largely on its implementation at Pfizer. We also discuss the opportunities afforded by emerging technological advances in cryo-EM, and the prospects for future development of the technique.

scholarly journals Applications of X-ray Powder Diffraction in Protein Crystallography and Drug Screening

Crystals ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 54 ◽  
Author(s):  
Maria Spiliopoulou ◽  
Alexandros Valmas ◽  
Dimitris-Panagiotis Triandafillidis ◽  
Christos Kosinas ◽  
Andrew Fitch ◽  
...  
Keyword(s):  
Powder Diffraction ◽  
Structural Characterization ◽  
Three Dimensional ◽  
Drug Formulation ◽  
Biological Macromolecules ◽  
Structure Based Drug Design ◽  
X Ray ◽  
Structural Modifications ◽  
Fundamental Information

Providing fundamental information on intra/intermolecular interactions and physicochemical properties, the three-dimensional structural characterization of biological macromolecules is of extreme importance towards understanding their mechanism of action. Among other methods, X-ray powder diffraction (XRPD) has proved its applicability and efficiency in numerous studies of different materials. Owing to recent methodological advances, this method is now considered a respectable tool for identifying macromolecular phase transitions, quantitative analysis, and determining structural modifications of samples ranging from small organics to full-length proteins. An overview of the XRPD applications and recent improvements related to the study of challenging macromolecules and peptides toward structure-based drug design is discussed. This review congregates recent studies in the field of drug formulation and delivery processes, as well as in polymorph identification and the effect of ligands and environmental conditions upon crystal characteristics. These studies further manifest the efficiency of protein XRPD for quick and accurate preliminary structural characterization.

scholarly journals Structural Characterization of Heterodinuclear ZnII-LnIII Complexes (Ln = Pr, Nd) with a Ring-Contracted H2valdien-Derived Schiff Base Ligand

2021 ◽  
Author(s):  
Shabana Noor ◽  
Richard Goddard ◽  
Fehmeeda Khatoon ◽  
Sarvendra Kumar ◽  
Rüdiger W. Seidel
Keyword(s):  
Molecular Structure ◽  
Schiff Base ◽  
Structural Characterization ◽  
Schiff Base Ligand ◽  
Crystal And Molecular Structure ◽  
X Ray ◽  
X Ray Crystallography ◽  
Imidazoline Ring

AbstractSynthesis and structural characterization of two heterodinuclear ZnII-LnIII complexes with the formula [ZnLn(HL)(µ-OAc)(NO3)2(H2O)x(MeOH)1-x]NO3 · n H2O · n MeOH [Ln = Pr (1), Nd (2)] and the crystal and molecular structure of [ZnNd(HL)(µ-OAc)(NO3)2(H2O)] [ZnNd(HL)(OAc)(NO3)2(H2O)](NO3)2 · n H2O · n MeOH (3) are reported. The asymmetrical compartmental ligand (E)-2-(1-(2-((2-hydroxy-3-methoxybenzylidene)amino)-ethyl)imidazolidin-2-yl)-6-methoxyphenol (H2L) is formed from N1,N3-bis(3-methoxysalicylidene)diethylenetriamine (H2valdien) through intramolecular aminal formation, resulting in a peripheral imidazoline ring. The structures of 1–3 were revealed by X-ray crystallography. The smaller ZnII ion occupies the inner N2O2 compartment of the ligand, whereas the larger and more oxophilic LnIII ions are found in the outer O2O2’ site. Graphic Abstract Synthesis and structural characterization of two heterodinuclear ZnII-LnIII complexes (Ln = Pr, Nd) bearing an asymmetrical compartmental ligand formed in situ from N1,N3-bis(3-methoxysalicylidene)diethylenetriamine (H2valdien) through intramolecular aminal formation are reported.

Synthesis and structural characterization of a magnesium phthalocyanine(3–) anion

2012 ◽  
Vol 16 (01) ◽  
pp. 154-162 ◽  
Author(s):  
Edwin W.Y. Wong ◽  
Daniel B. Leznoff
Keyword(s):  
Absorption Spectrum ◽  
Solid State ◽  
Single Crystal ◽  
Structural Characterization ◽  
Heterometallic Complex ◽  
State Structure ◽  
Solid State Structure ◽  
X Ray ◽  
X Ray Crystallography

The reduction of magnesium phthalocyanine (MgPc) with 2.2 equivalents of potassium graphite in 1,2-dimethoxyethane (DME) gives [K2(DME)4]PcMg(OH)(1) in 67% yield. Compound 1 was structurally characterized using single crystal X-ray crystallography and was found to be a monomeric, heterometallic complex consisting of a μ3-OH ligand that bridges a [MgIIPc3-]- anion to two potassium cations solvated by four DME molecules. An absorption spectrum of 1 confirms the Pc ligand is singly reduced and has a 3–charge. The solid-state structure of 1 does not indicate breaking of the aromaticity of the Pc ligand. Compound 1 is only the second Pc3- complex and the first reduced MgPc to be isolated and structurally characterized.

scholarly journals Structure-Based Drug Design and Characterization of Sulfonyl-Piperazine Benzothiazinone Inhibitors of DprE1 from Mycobacterium tuberculosis

2018 ◽  
Vol 62 (10) ◽  
Author(s):  
Jérémie Piton ◽  
Anthony Vocat ◽  
Andréanne Lupien ◽  
Caroline S. Foo ◽  
Olga Riabova ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Drug Design ◽  
Antitubercular Activity ◽  
Cysteine Residue ◽  
Drug Candidate ◽  
Structure Based Drug Design ◽  
Content Type ◽  
Active Site Cysteine ◽  
Covalent Adducts

ABSTRACT Macozinone (MCZ) is a tuberculosis (TB) drug candidate that specifically targets the essential flavoenzyme DprE1, thereby blocking synthesis of the cell wall precursor decaprenyl phosphoarabinose (DPA) and provoking lysis of Mycobacterium tuberculosis. As part of the MCZ backup program, we exploited structure-guided drug design to produce a new series of sulfone-containing derivatives, 2-sulfonylpiperazin 8-nitro 6-trifluoromethyl 1,3-benzothiazin-4-one, or sPBTZ. These compounds are less active than MCZ but have a better solubility profile, and some derivatives display enhanced stability in microsomal assays. DprE1 was efficiently inhibited by sPBTZ, and covalent adducts with the active-site cysteine residue (C387) were formed. However, despite the H-bonding potential of the sulfone group, no additional bonds were seen in the crystal structure of the sPBTZ-DprE1 complex with compound 11326127 compared to MCZ. Compound 11626091, the most advanced sPBTZ, displayed good antitubercular activity in the murine model of chronic TB but was less effective than MCZ. Nonetheless, further testing of this MCZ backup compound is warranted as part of combination treatment with other TB drugs.

scholarly journals Structural characterization of alloxazine and substituted isoalloxazines: NMR and X-ray crystallography

ARKIVOC ◽  
2006 ◽  
Vol 2007 (4) ◽  
pp. 20-38 ◽  
Author(s):  
Mª Ángeles Farrán ◽  
Rosa Mª Claramunt ◽  
Concepción López ◽  
Elena Pinilla ◽  
Mª Rosario Torres ◽  
...  
Keyword(s):  
Structural Characterization ◽  
X Ray ◽  
X Ray Crystallography

scholarly journals High-Resolution Analysis of Zn2+ Coordination in the Alkaline Phosphatase Superfamily by EXAFS and X-ray Crystallography

2012 ◽  
Vol 415 (1) ◽  
pp. 102-117 ◽  
Author(s):  
Elena Bobyr ◽  
Jonathan K. Lassila ◽  
Helen I. Wiersma-Koch ◽  
Timothy D. Fenn ◽  
Jason J. Lee ◽  
...  
Keyword(s):  
Alkaline Phosphatase ◽  
High Resolution ◽  
X Ray ◽  
X Ray Crystallography ◽  
High Resolution Analysis ◽  
Resolution Analysis

Structural characterization of a fluorescein hydrazone molecular switch with application towards logic gates

2018 ◽  
Vol 42 (22) ◽  
pp. 18050-18058 ◽  
Author(s):  
Juan D. Villada ◽  
Richard F. D’Vries ◽  
Mario Macías ◽  
Fabio Zuluaga ◽  
Manuel N. Chaur
Keyword(s):  
Structural Characterization ◽  
Metal Cations ◽  
Logic Gates ◽  
Molecular Switch ◽  
Logic Circuits ◽  
X Ray ◽  
Ph Changes ◽  
X Ray Crystallography ◽  
Half Adder

A new polymorph of fluorescein hydrazone was fully characterized via single X-ray crystallography. In addition, multiple logic circuits and a Half-Adder operator were designed using the fluorescence and UV-Vis switching responses of the fluorescein compound to different metal cations and pH changes.

scholarly journals The critical role of QM/MM X-ray refinement and accurate tautomer/protomer determination in structure-based drug design

2020 ◽  
Author(s):  
Oleg Y. Borbulevych ◽  
Roger I. Martin ◽  
Lance M. Westerhoff
Keyword(s):  
Drug Design ◽  
Critical Role ◽  
Pharmaceutical Research ◽  
Energy Functional ◽  
Structural Refinement ◽  
Structure Based Drug Design ◽  
X Ray ◽  
X Ray Crystallography ◽  
Refinement Method ◽  
The Impact

Abstract Conventional protein:ligand crystallographic refinement uses stereochemistry restraints coupled with a rudimentary energy functional to ensure the correct geometry of the model of the macromolecule—along with any bound ligand(s)—within the context of the experimental, X-ray density. These methods generally lack explicit terms for electrostatics, polarization, dispersion, hydrogen bonds, and other key interactions, and instead they use pre-determined parameters (e.g. bond lengths, angles, and torsions) to drive structural refinement. In order to address this deficiency and obtain a more complete and ultimately more accurate structure, we have developed an automated approach for macromolecular refinement based on a two layer, QM/MM (ONIOM) scheme as implemented within our DivCon Discovery Suite and "plugged in" to two mainstream crystallographic packages: PHENIX and BUSTER. This implementation is able to use one or more region layer(s), which is(are) characterized using linear-scaling, semi-empirical quantum mechanics, followed by a system layer which includes the balance of the model and which is described using a molecular mechanics functional. In this work, we applied our Phenix/DivCon refinement method—coupled with our XModeScore method for experimental tautomer/protomer state determination—to the characterization of structure sets relevant to structure-based drug design (SBDD). We then use these newly refined structures to show the impact of QM/MM X-ray refined structure on our understanding of function by exploring the influence of these improved structures on protein:ligand binding affinity prediction (and we likewise show how we use post-refinement scoring outliers to inform subsequent X-ray crystallographic efforts). Through this endeavor, we demonstrate a computational chemistry ↔ structural biology (X-ray crystallography) "feedback loop" which has utility in industrial and academic pharmaceutical research as well as other allied fields.

Activation of C–Cl Bonds: Synthesis and Structural Characterization of [Ru2(μ-Cl)(μ-PtBu2)(μ- Ph2PN(H)PPh2)(CO)4]

2013 ◽  
Vol 68 (5-6) ◽  
pp. 743-746 ◽  
Author(s):  
Tobias Mayer ◽  
Hans-Christian Böttcher
Keyword(s):  
Carbon Tetrachloride ◽  
Single Crystals ◽  
Structural Characterization ◽  
Title Compound ◽  
X Ray ◽  
X Ray Crystallography ◽  
High Yields

The synthesis and structural characterization of the complex [Ru2(μ-Cl)(μ-PtBu2)(μ-dppa)(CO)4] (4, dppa = Ph2PN(H)PPh2) are reported. The title compound and two other related complexes were obtained in high yields by the reaction of the coordinatively unsaturated species [Ru2(μ-H)(μ-PtBu2)(μ-PˆP)(CO)4] (PˆP = dppa, 3; PˆP =Ph2PN(Ph)PPh2, 5; PˆP =Ph2PN(CH2Ph)PPh2, 6) with carbon tetrachloride. Single crystals of 4 grown from dichloromethane-acetone have been analyzed by X-ray crystallography

scholarly journals Modulation of Amyloidogenic Protein Self-Assembly Using Tethered Small Molecules

2020 ◽  
Author(s):  
Emma Cawood ◽  
Nicolas Guthertz ◽  
Jessica Ebo ◽  
Theodoros Karamanos ◽  
Sheena E. Radford FRS ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Structural Characterization ◽  
Self Assembly ◽  
Molecular Mechanisms ◽  
Amyloid Fibrils ◽  
Fibril Formation ◽  
X Ray Crystallography ◽  
Starting Point ◽  
Amyloid Assembly

<p></p><p>Protein-protein interactions (PPIs) are involved in many of life’s essential biological functions yet are also an underlying cause of several human diseases, including amyloidosis. The modulation of PPIs presents opportunities to gain mechanistic insights into amyloid assembly, particularly through the use of methods which can trap specific intermediates for detailed study. Such information can also provide a starting point for drug discovery. Here, we demonstrate that covalently tethered small molecule fragments can be used to stabilize specific oligomers during amyloid fibril formation, facilitating the structural characterization of these assembly intermediates. We exemplify the power of covalent tethering using the naturally occurring truncated variant (ΔN6) of the human protein β2-microglobulin (β2m), which assembles into amyloid fibrils associated with dialysis-related amyloidosis. Using this approach, we have trapped tetramers formed by ΔN6 under conditions which would normally lead to fibril formation and found that the degree of tetramer stabilization depends on the site of the covalent tether and the nature of the protein-fragment interaction. The covalent protein-ligand linkage enabled structural characterization of these trapped oligomeric species using X-ray crystallography and NMR, providing insight into why tetramer stabilization inhibits amyloid assembly. Our findings highlight the power of “post-translational chemical modification" as a tool to study biological molecular mechanisms. </p><br><p></p>

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