How Do Microbial Metabolites Interact with Their Protein Targets? DOI

Mario Astigarraga,

Andrés Sánchez-Ruiz,

Aminata Diop-Aw

et al.

Journal of Chemical Information and Modeling, Journal Year: 2025, Volume and Issue: 65(1), P. 201 - 213

Published: Jan. 2, 2025

The design of drugs and nutraceutics that mimic microbial metabolites is an emerging drug modality in medicinal chemistry attempts to modulate the myriad interactions these molecules establish with host proteins. Understanding how interact their target proteins key perform a rational metabolite mimetic for therapeutic usage. In present work, we address this question by analyzing functional groups they display set more than 71K protein–metabolite from PDB. Significant differences group distributions, chemical features, co-occurrences are observed distinct subsets molecules. same true distributions interaction types. By correlating both data sets, able explain patterns terms patterns. These results will shed light on novel purposes.

Language: Английский

Transition-Metal-Catalyzed C–S, C–Se, and C–Te Bond Formations via Cross-Coupling and Atom-Economic Addition Reactions. Achievements and Challenges DOI
I. P. Beletskaya, Valentine P. Ananikov

Chemical Reviews, Journal Year: 2022, Volume and Issue: 122(21), P. 16110 - 16293

Published: Sept. 16, 2022

In the present review, we discuss recent progress in field of C–Z bond formation reactions (Z = S, Se, Te) catalyzed by transition metals. Two complementary methodologies are considered─catalytic cross-coupling and catalytic addition reactions. The development advanced systems is aimed at improved catalyst efficiency, reduced loading, better cost environmental concerns, higher selectivity yields. important rise research efforts sustainability green chemistry areas critically assessed. paramount role mechanistic studies a new generation addressed, key achievements, problems, challenges summarized for this field.

Language: Английский

Citations

201

Enzymatic Late‐Stage Modifications: Better Late Than Never DOI Creative Commons
Elvira Romero, Bethan S. Jones, Bethany N. Hogg

et al.

Angewandte Chemie International Edition, Journal Year: 2021, Volume and Issue: 60(31), P. 16824 - 16855

Published: Jan. 16, 2021

Enzyme catalysis is gaining increasing importance in synthetic chemistry. Nowadays, the growing number of biocatalysts accessible by means bioinformatics and enzyme engineering opens up an immense variety selective reactions. Biocatalysis especially provides excellent opportunities for late-stage modification often superior to conventional de novo synthesis. Enzymes have proven be useful direct introduction functional groups into complex scaffolds, as well rapid diversification compound libraries. Particularly important highly topical are enzyme-catalysed oxyfunctionalisations, halogenations, methylations, reductions, amide bond formations due high prevalence these motifs pharmaceuticals. This Review gives overview strengths limitations enzymatic modifications using native engineered enzymes synthesis while focusing on examples drug development.

Language: Английский

Citations

117

Decatungstate-Catalyzed C(sp3)–H Sulfinylation: Rapid Access to Diverse Organosulfur Functionality DOI
Patrick Sarver, Noah B. Bissonnette, David W. C. MacMillan

et al.

Journal of the American Chemical Society, Journal Year: 2021, Volume and Issue: 143(26), P. 9737 - 9743

Published: June 23, 2021

Here we report the direct conversion of strong, aliphatic C(

Language: Английский

Citations

117

Replacement of Less-Preferred Dipolar Aprotic and Ethereal Solvents in Synthetic Organic Chemistry with More Sustainable Alternatives DOI Creative Commons
Andrew Jordan, Callum G. J. Hall,

Lee R. Thorp

et al.

Chemical Reviews, Journal Year: 2022, Volume and Issue: 122(6), P. 6749 - 6794

Published: Feb. 24, 2022

Dipolar aprotic and ethereal solvents comprise just over 40% of all organic utilized in synthetic organic, medicinal, process chemistry. Unfortunately, many the common "go-to" are considered to be "less-preferable" for a number environmental, health, safety (EHS) reasons such as toxicity, mutagenicity, carcinogenicity, or practical handling flammability volatility. Recent legislative changes have initiated implementation restrictions on use commonly employed dipolar dimethylformamide (DMF) N-methyl-2-pyrrolidinone (NMP), ethers 1,4-dioxane. Thus, with growing legislative, EHS, societal pressures, need identify implement alternative that greener, safer, more sustainable has never been greater. Within this review, ubiquitous nature is discussed respect physicochemical properties made them so appealing chemists. An overview current being imposed discussed. A variety alternative, garnered attention past decade then examined, case studies examples where less-preferable successfully replaced safer highlighted. Finally, general guidance solvent selection replacement included Supporting Information review.

Language: Английский

Citations

113

“Magic Chloro”: Profound Effects of the Chlorine Atom in Drug Discovery DOI
Debora Chiodi, Yoshihiro Ishihara

Journal of Medicinal Chemistry, Journal Year: 2023, Volume and Issue: 66(8), P. 5305 - 5331

Published: April 4, 2023

Chlorine is one of the most common atoms present in small-molecule drugs beyond carbon, hydrogen, nitrogen, and oxygen. There are currently more than 250 FDA-approved chlorine-containing drugs, yet beneficial effect chloro substituent has not been reviewed. The seemingly simple substitution a hydrogen atom (R = H) with chlorine Cl) can result remarkable improvements potency up to 100,000-fold lead profound effects on pharmacokinetic parameters including clearance, half-life, drug exposure vivo. Following literature terminology "magic methyl effect" term coined herein. Although reports 500-fold or 1000-fold often serendipitous discoveries that be considered "magical" rather planned, hypotheses made explain magic lessons accelerate cycle discovery.

Language: Английский

Citations

112

Green metrics in mechanochemistry DOI Creative Commons

Nicolas Fantozzi,

Jean‐Noël Volle, Andrea Porcheddu

et al.

Chemical Society Reviews, Journal Year: 2023, Volume and Issue: 52(19), P. 6680 - 6714

Published: Jan. 1, 2023

The quantitative assessment of the greenness mechanochemical processes for green metrics were calculated is herein reported. A general introduction to topic, variables influencing reaction outcome and, an outlook are also provided.

Language: Английский

Citations

87

Knowledge graph-enhanced molecular contrastive learning with functional prompt DOI Creative Commons
Fang Yin, Qiang Zhang, Ningyu Zhang

et al.

Nature Machine Intelligence, Journal Year: 2023, Volume and Issue: 5(5), P. 542 - 553

Published: May 4, 2023

Abstract Deep learning models can accurately predict molecular properties and help making the search for potential drug candidates faster more efficient. Many existing methods are purely data driven, focusing on exploiting intrinsic topology construction rules of molecules without any chemical prior information. The high dependency makes them difficult to generalize a wider space leads lack interpretability predictions. Here, address this issue, we introduce element-oriented knowledge graph summarize basic elements their closely related functional groups. We further propose method graph-enhanced contrastive with prompt (KANO), external fundamental domain in both pre-training fine-tuning. Specifically, as prior, first design an element-guided augmentation contrastive-based explore microscopic atomic associations violating semantics. Then, learn prompts fine-tuning evoke downstream task-related acquired by pre-trained model. Extensive experiments show that KANO outperforms state-of-the-art baselines 14 property prediction datasets provides chemically sound explanations its This work contributes efficient offering high-quality interpretable representation superior performance.

Language: Английский

Citations

84

Multi-modal molecule structure–text model for text-based retrieval and editing DOI
Shengchao Liu, Weili Nie, Chengpeng Wang

et al.

Nature Machine Intelligence, Journal Year: 2023, Volume and Issue: 5(12), P. 1447 - 1457

Published: Dec. 18, 2023

Language: Английский

Citations

62

Ni(II)-MOF based hypersensitive dual-function luminescent sensor towards 3-nitrotyrosine biomarker and 6-Propyl-2-thiouracil antithyroid drug in Urine DOI
Wen‐Cui Li, Liying Liu, Xiaoting Li

et al.

Journal of Materials Chemistry B, Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 1, 2024

Luminescent NiMOF demonstrated remarkable capabilities in efficient, sensitive and intelligent detection of 3-NT biomarker 6-PTU thyroid drug urine through luminescence quenching effects.

Language: Английский

Citations

31

Expanding chemistry through in vitro and in vivo biocatalysis DOI
Elijah N. Kissman, Max B. Sosa,

Douglas C Millar

et al.

Nature, Journal Year: 2024, Volume and Issue: 631(8019), P. 37 - 48

Published: July 3, 2024

Language: Английский

Citations

30