scholarly journals Hydrazines as versatile chemical biology probes and drug-discovery tools for cofactor-dependent enzymes

2020 ◽  
Author(s):  
Zongtao Lin ◽  
Xie Wang ◽  
Katelyn A Bustin ◽  
Lin He ◽  
Radu M Suciu ◽  
...  
Keyword(s):  
Drug Discovery ◽  
Active Site ◽  
Chemical Biology ◽  
Tissue Imaging ◽  
Single Type ◽  
Functional Classes ◽  
The Common ◽  
Enzyme Cofactors ◽  
Transient Intermediates ◽  
Substituted Hydrazines

Known chemoproteomic probes generally use warheads that tag a single type of amino acid or modified form thereof to identify cases in which its hyper-reactivity underpins function. Much important biochemistry derives from electron-poor enzyme cofactors, transient intermediates and chemically-labile regulatory modifications, but probes for such species are underdeveloped. Here, we have innovated a versatile class of chemoproteomic probes for this less charted hemisphere of the proteome by using hydrazine as the common chemical warhead. Its electron-rich nature allows it to react by both polar and radicaloid mechanisms and to target multiple, pharmacologically important functional classes of enzymes bearing diverse organic and inorganic cofactors. Probe attachment can be blocked by active-site-directed inhibitors, and elaboration of the warhead supports connection of a target to a lead compound. The capacity of substituted hydrazines to profile, discover and inhibit diverse cofactor-dependent enzymes enables cell and tissue imaging and makes this platform useful for enzyme and drug discovery.

scholarly journals Enzyme–Inhibitor Interactions and a Simple, Rapid Method for Determining Inhibition Modality

2019 ◽  
Vol 24 (5) ◽  
pp. 515-522 ◽  
Author(s):  
Shane M. Buker ◽  
P. Ann Boriack-Sjodin ◽  
Robert A. Copeland
Keyword(s):  
Drug Discovery ◽  
Substrate Concentration ◽  
Chemical Biology ◽  
Enzyme Inhibitor ◽  
Specific Inhibition ◽  
Experimental Conditions ◽  
The Common ◽  
Inhibitory Molecules ◽  
The Impact

Contemporary chemical biology and drug discovery are increasingly focused on the discovery of inhibitory molecules that interact with enzyme targets in specific ways, such as allosteric or orthosteric binding. Hence, there is increasing interest in evaluating hit compounds from high-throughput diversity screening to determine their mode of interaction with the target. In this work, the common inhibition modalities are reviewed and clarified. The impact of substrate concentration, relative to substrate KM, for each common inhibition modality is also reviewed. The pattern of changes in IC50 that accompany increasing substrate concentration are shown to be diagnostic of specific inhibition modalities. Thus, replots of IC50 as a function of the ratio [S]/KM are recommended as a simple and rapid means of assessing inhibition modality. Finally, specific recommendations are offered for ideal experimental conditions for the determination of inhibition modality through the use of IC50 replots.

Exploring the Chemistry and Therapeutic Potential of Triazoles: A Comprehensive Literature Review

2019 ◽  
Vol 19 (16) ◽  
pp. 1298-1368 ◽  
Author(s):  
Ankit Jain ◽  
Poonam Piplani
Keyword(s):  
Oxidative Stress ◽  
Drug Discovery ◽  
Literature Review ◽  
Structural Modification ◽  
Therapeutic Potential ◽  
Pharmacological Properties ◽  
Pharmacological Activities ◽  
Triazole Derivatives ◽  
Comprehensive Literature Review ◽  
The Common

: Triazole is a valuable platform in medicinal chemistry, possessing assorted pharmacological properties, which could play a major role in the common mechanisms associated with various disorders like cancer, infections, inflammation, convulsions, oxidative stress and neurodegeneration. Structural modification of this scaffold could be helpful in the generation of new therapeutically useful agents. Although research endeavors are moving towards the growth of synthetic analogs of triazole, there is still a lot of scope to achieve drug discovery break-through in this area. Upcoming therapeutic prospective of this moiety has captured the attention of medicinal chemists to synthesize novel triazole derivatives. The authors amalgamated the chemistry, synthetic strategies and detailed pharmacological activities of the triazole nucleus in the present review. Information regarding the marketed triazole derivatives has also been incorporated. The objective of the review is to provide insights to designing and synthesizing novel triazole derivatives with advanced and unexplored pharmacological implications.

Experimental and Computational Approaches to Improve Binding Affinity in Chemical Biology and Drug Discovery

2020 ◽  
Vol 20 (19) ◽  
pp. 1651-1660
Author(s):  
Anuraj Nayarisseri
Keyword(s):  
Drug Discovery ◽  
Drug Design ◽  
Binding Affinity ◽  
Chemical Biology ◽  
De Novo ◽  
Structure Based Drug Design ◽  
Computational Approaches ◽  
Drug Designing ◽  
Traditional Drug ◽  
Computer Based

Drug discovery is one of the most complicated processes and establishment of a single drug may require multidisciplinary attempts to design efficient and commercially viable drugs. The main purpose of drug design is to identify a chemical compound or inhibitor that can bind to an active site of a specific cavity on a target protein. The traditional drug design methods involved various experimental based approaches including random screening of chemicals found in nature or can be synthesized directly in chemical laboratories. Except for the long cycle design and time, high cost is also the major issue of concern. Modernized computer-based algorithm including structure-based drug design has accelerated the drug design and discovery process adequately. Surprisingly from the past decade remarkable progress has been made concerned with all area of drug design and discovery. CADD (Computer Aided Drug Designing) based tools shorten the conventional cycle size and also generate chemically more stable and worthy compounds and hence reduce the drug discovery cost. This special edition of editorial comprises the combination of seven research and review articles set emphasis especially on the computational approaches along with the experimental approaches using a chemical synthesizing for the binding affinity in chemical biology and discovery as a salient used in de-novo drug designing. This set of articles exfoliates the role that systems biology and the evaluation of ligand affinity in drug design and discovery for the future.

scholarly journals An enzymatic activation of formaldehyde for nucleotide methylation

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Charles Bou-Nader ◽  
Frederick W. Stull ◽  
Ludovic Pecqueur ◽  
Philippe Simon ◽  
Vincent Guérineau ◽  
...  
Keyword(s):  
Amino Acids ◽  
Thymidylate Synthase ◽  
Active Site ◽  
De Novo ◽  
Crystallographic Structure ◽  
De Novo Synthesis ◽  
Active Site Residues ◽  
Enzymatic Activation ◽  
Enzyme Cofactors ◽  
Unique Ability

AbstractFolate enzyme cofactors and their derivatives have the unique ability to provide a single carbon unit at different oxidation levels for the de novo synthesis of amino-acids, purines, or thymidylate, an essential DNA nucleotide. How these cofactors mediate methylene transfer is not fully settled yet, particularly with regard to how the methylene is transferred to the methylene acceptor. Here, we uncovered that the bacterial thymidylate synthase ThyX, which relies on both folate and flavin for activity, can also use a formaldehyde-shunt to directly synthesize thymidylate. Combining biochemical, spectroscopic and anaerobic crystallographic analyses, we showed that formaldehyde reacts with the reduced flavin coenzyme to form a carbinolamine intermediate used by ThyX for dUMP methylation. The crystallographic structure of this intermediate reveals how ThyX activates formaldehyde and uses it, with the assistance of active site residues, to methylate dUMP. Our results reveal that carbinolamine species promote methylene transfer and suggest that the use of a CH2O-shunt may be relevant in several other important folate-dependent reactions.

Syntheses of Spiro(2-oxopyrrolidinyl)-5,4′-pyrazolones via Organocatalyzed Michael/Ammonolysis Cascade Reaction of 4-Aminopyrazolones and α,β-Unsaturated Acyl Phosphates

Synlett ◽  
2021 ◽  
Author(s):  
Lin Chen ◽  
You-Fen Li ◽  
Zheng-Jun Chen ◽  
Wen-Ya Jiao ◽  
Zhi-Jiao Chen
Keyword(s):  
Drug Discovery ◽  
Chemical Biology ◽  
Cascade Reaction ◽  
Unsaturated Acyl

AbstractThe efficient organocatalyzed Michael/ammonolysis cascade reaction of N-protected 4-aminopyrazolones and α,β-unsaturated acyl phosphates has been developed. This tactic gives rise to architecturally multifarious spiro(2-oxopyrrolidinyl)-5,4′-pyrazolones in good productiveness (up to 88% yield) and with moderate to good diastereoselectivities (up to 20:1 dr). These novel hybrid heterocycles would be promising candidates for drug-discovery programs and chemical biology.

scholarly journals XIV. On the structure and development of the wing in the common fowl

1888 ◽  
Vol 179 ◽  
pp. 385-398 ◽  
Keyword(s):  
Single Type ◽  
Short Paper ◽  
Type I ◽  
Single Region ◽  
The Common

Of late years, while the structure of the skull has greatly occupied me, the rest of the skeleton has been neglected in comparison. A quarter of a century ago, or more, the whole skeleton, in Birds especially, occupied much of my thought; and from an even earlier period I have never ceased to gather together embryos and young Birds of all kinds, which should some day serve for a renewal of the work. In this short paper, dealing with a single region, and that principally in a single type, I give the first-fruits of a revised study of the Bird’s skeleton. Many recent workers have dealt with the development of one part or other of the Bird’s wing ; but it seemed to me that we had from none of them a minute account of the successive changes in any one form. And now, having made such a study, I think I have not failed to draw some new facts from it.

scholarly journals High-resolution structures of inhibitor complexes of human indoleamine 2,3-dioxygenase 1 in a new crystal form

2018 ◽  
Vol 74 (11) ◽  
pp. 717-724 ◽  
Author(s):  
Shukun Luo ◽  
Ke Xu ◽  
Shaoyun Xiang ◽  
Jie Chen ◽  
Chunyun Chen ◽  
...  
Keyword(s):  
Drug Discovery ◽  
High Resolution ◽  
Crystal Structures ◽  
Active Site ◽  
Crystal Form ◽  
Crystal Forms ◽  
Cellular Processes ◽  
Potential Target ◽  
Indoleamine 2,3 Dioxygenase

Human indoleamine 2,3-dioxygenase 1 (IDO1) is a heme-dependent enzyme with important roles in many cellular processes and is a potential target for drug discovery against cancer and other diseases. Crystal structures of IDO1 in complex with various inhibitors have been reported. Many of these crystals belong to the same crystal form and most of the reported structures have resolutions in the range 3.2–2.3 Å. Here, three new crystal forms of human IDO1 obtained by introducing a surface mutation, K116A/K117A, distant from the active site are reported. One of these crystal forms diffracted to 1.5 Å resolution and can be readily used for soaking experiments to determine high-resolution structures of IDO1 in complex with the substrate tryptophan or inhibitors that coordinate the heme. In addition, this mutant was used to produce crystals of a complex with an inhibitor that targets the apo form of the enzyme under the same conditions; the structure of this complex was determined at 1.7 Å resolution. Overall, this mutant represents a robust platform for determining the structures of inhibitor and substrate complexes of IDO1 at high resolution.

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