ABSTRACT
We report a fast-track computationally driven discovery of new SARS-CoV-2 main protease (Mpro) inhibitors whose potency ranges from mM for the initial non-covalent ligands to sub-µM for the final covalent compound (IC50 = 830 ± 50 nM). The project extensively relied on high-resolution all-atom molecular dynamics simulations and absolute binding free energy calculations performed using the polarizable AMOEBA force field. The study is complemented by extensive adaptive sampling simulations that are used to rationalize the different ligand binding poses through the explicit reconstruction of the ligand-protein conformation space. Machine learning predictions are also performed to predict selected compound properties. While simulations extensively use high performance computing to strongly reduce the time-to-solution, they were systematically coupled to nuclear magnetic resonance experiments to drive synthesis and for in vitro characterization of compounds. Such a study highlights the power of in silico strategies that rely on structure-based approaches for drug design and allows the protein conformational multiplicity problem to be addressed. The proposed fluorinated tetrahydroquinolines open routes for further optimization of Mpro inhibitors towards low nM affinities.
ABSTRACT
Approximately two percent of the world's energy is consumed in the production of ammonia from hydrogen and nitrogen gas. Ammonia is used as a fertilizer ingredient for agriculture and distributed in the environment on an enormous scale to promote crop growth in intensive farming. Only 30-50 % of the nitrogen applied is assimilated by crop plants; the remaining 50-70 % goes into biological processes such as nitrification by microbial metabolism in the soil. This leads to an imbalance in the global nitrogen cycle and higher nitrous oxide emissions (a potent and significant greenhouse gas) as well as contamination of ground and surface waters by nitrate from the nitrogen-fertilized farmland. This Review gives a critical overview of the current knowledge of soil microbes involved in the chemistry of ammonia nitrification, the structures and mechanisms of the enzymes involved, and phytochemicals capable of inhibiting ammonia nitrification.
Subject(s)
Ammonium Compounds/metabolism , Soil Microbiology , Soil/chemistry , Nitrates/metabolism , Nitrobacter/metabolism , Nitrogen Cycle , Nitrous Oxide/metabolism , Oxidation-Reduction , Oxidoreductases/chemistry , Oxidoreductases/metabolism , Plants/metabolismABSTRACT
Pyrabactin resistance 1 (PYR1) and related abscisic acid (ABA) receptors are new targets for manipulating plant drought tolerance. Here, we identify and use PYR1 hypersensitive mutants to define ligand binding hotspots and show that these can guide improvements in agonist potency. One hotspot residue defined, A160, is part of a pocket that is occupied by ABA's C6 methyl or by the toluyl methyl of the synthetic agonist quinabactin (QB). A series of QB analogues substituted at the toluyl position were synthesized and provide up to 10-fold gain in activity in vitro. Furthermore, we demonstrate that hypersensitive receptors can be used to improve the sensitivity of a previously described mammalian cell ABA-regulated transcriptional circuit by three orders of magnitude. Collectively, our data show that the systematic mapping of hypersensitivity sites in a ligand-binding pocket can help guide ligand optimization and tune the sensitivity of engineered receptors.
Subject(s)
Arabidopsis Proteins/agonists , Quinolones/chemistry , Quinolones/metabolism , Sulfonamides/chemistry , Sulfonamides/metabolism , Arabidopsis/metabolism , Arabidopsis Proteins/metabolism , Gene Expression Regulation, Plant , Ligands , Membrane Transport Proteins/metabolism , Molecular Dynamics Simulation , Plants, Genetically Modified/metabolismABSTRACT
Microtubule-targeting agents (MTAs) are some of the clinically most successful anti-cancer drugs. Unfortunately, instances of multidrug resistances to MTA have been reported, which highlights the need for developing MTAs with different mechanistic properties. One less explored class of MTAs are [1,2,4]triazolo[1,5-a]pyrimidines (TPs). These cytotoxic compounds are microtubule-stabilizing agents that inexplicably bind to vinblastine binding site on tubulin, which is typically targeted by microtubule-destabilizing agents. Here we used cellular, biochemical, and structural biology approaches to address this apparent discrepancy. Our results establish TPs as vinca-site microtubule-stabilizing agents that promote longitudinal tubulin contacts in microtubules, in contrast to classical microtubule-stabilizing agents that primarily promote lateral contacts. Additionally we observe that TPs studied here are not affected by p-glycoprotein overexpression, and suggest that TPs are promising ligands against multidrug-resistant cancer cells.
Subject(s)
Microtubules/drug effects , Microtubules/metabolism , Pyrimidines/pharmacology , Triazoles/pharmacology , Tubulin/metabolism , Vinca Alkaloids/metabolism , Binding Sites , Cell Line, Tumor , Humans , Ligands , Models, Molecular , Protein Multimerization/drug effects , Protein Structure, Quaternary , Tubulin/chemistryABSTRACT
Seed germination and early seedling development are essential events in the plant life cycle that are controlled largely by the interplay and cross-talk between several plant hormones. Recently, major progress has been achieved in the elucidation at the molecular level of the signalling of these phytohormones. In this review, we summarise the data for the most promising classes of compounds, which could find potential agronomic applications for promoting seed germination and early seedling development even under abiotic stress conditions. Structural modifications of plant hormones are required to improve their biological performance and their specificity to allow commercial application.
Subject(s)
Germination/drug effects , Seedlings/drug effects , SeedsABSTRACT
A novel class of experimental fungicides has been discovered, which consists of special tetrasubstituted imidazoles. They are highly active against important phytopathogens, such as Botrytis cinerea (grey mould), Uncinula necator (grape powdery mildew), Mycosphaerella graminicola (wheat leaf blotch) and Alternaria solani (potato and tomato early blight). Their fungicidal efficacy is due to their ability to promote fungal tubulin polymerization, which leads to a disruption of microtubule dynamics. These imidazoles are five-membered ring analogs of similar substituted triazolopyrimidines and pyridazines with the same mode of action. A concise four-step synthesis route has been used to prepare them from commercially available starting materials.
Subject(s)
Fungicides, Industrial/chemistry , Fungicides, Industrial/pharmacology , Imidazoles/chemistry , Imidazoles/pharmacology , Plant Diseases/microbiology , Tubulin Modulators/chemistry , Tubulin Modulators/pharmacology , Alternaria/drug effects , Ascomycota/drug effects , Botrytis/drug effects , Fungicides, Industrial/chemical synthesis , Imidazoles/chemical synthesis , Plant Proteins/metabolism , Plants/metabolism , Plants/microbiology , Tubulin/metabolism , Tubulin Modulators/chemical synthesisABSTRACT
Special tetrasubstituted pyridazines are potent fungicides by promoting the tubulin polymerisation, hereby disrupting the microtubule dynamics in the fungus. They are monocyclic analogs of similar substituted triazolopyrimidines and pyridopyrazines with the same mode of action. The fungicidal activity of these pyridazines was evaluated against the plant pathogens Botrytis cinerea (grey mould), Mycosphaerella graminicola (wheat leaf blotch) and Alternaria solani (potato and tomato early blight). Structure-activity relationship studies revealed the importance of a methyl and a chlorine substituent next to both ring nitrogen atoms and two aryl or heteroaryl groups in the other two pyridazine positions.
Subject(s)
Antifungal Agents/chemical synthesis , Antifungal Agents/pharmacology , Ascomycota/drug effects , Botrytis/drug effects , Pyridazines/chemistry , Pyridazines/pharmacology , Tubulin Modulators/chemical synthesis , Animals , Antifungal Agents/chemistry , Pyridazines/chemical synthesis , Structure-Activity Relationship , Swine , Tubulin Modulators/chemistry , Tubulin Modulators/pharmacologyABSTRACT
BACKGROUND: Pinoxaden is a new cereal herbicide that provides outstanding levels of post-emergence activity against a broad spectrum of grass weed species for worldwide selective use in both wheat and barley. RESULTS: Factors influencing activity and tolerance to pinoxaden were in part linked to distinct structural parts of the active ingredient. Three complementary contributions that decisively impact upon the herbicidal potency against grasses were identified: a preferred 2,6-diethyl-4-methyl aromatic substitution pattern, a dione area suitable for proherbicide formation and beneficial adjuvant effects. The uptake and translocation pattern of pinoxaden when coapplied with its tailored adjuvant were analysed by autoradiography, indicating extensive and rapid penetration, followed by effective distribution throughout the plant. Crop injury reduction on incorporation of the [1,4,5]oxadiazepane ring into the aryldione template was reinforced with safener technology. Comparative studies on the behaviour of pinoxaden applied either alone or in combination with the safener cloquintocet-mexyl demonstrated that addition of the safener resulted in significant enhancement of metabolic degradation in wheat and barley, providing excellent crop tolerance and a substantial selectivity margin without adverse effects on weed control. CONCLUSION: The biological potential of pinoxaden and its active principle pinoxaden dione in terms of grass weed control and tolerance in cereals was fully exploited by inclusion of the safener cloquintocet-mexyl in the formulation in combination with a specific and tailor-made tank-mix adjuvant based on methylated rape seed oil.
Subject(s)
Herbicides/chemistry , Heterocyclic Compounds, 2-Ring/chemistry , Poaceae/drug effects , Quinolines/pharmacology , Adjuvants, Pharmaceutic/chemistry , Adjuvants, Pharmaceutic/pharmacology , Autoradiography , Crystallography, X-Ray , Herbicide Resistance , Herbicides/pharmacology , Heterocyclic Compounds, 2-Ring/pharmacology , Plant Weeds/drug effects , Structure-Activity Relationship , Weed ControlABSTRACT
BACKGROUND: The excellent fungicidal activity of [1,2,4]triazolo[1,5-a]pyrimidines suggested the search for further analogues with improved properties. RESULTS: A series of novel trisubstituted pyrido[2,3-b]pyrazines has been designed and prepared as 6,6-biheterocyclic analogues of related 5,6-bicyclic [1,2,4]triazolo[1,5-a]pyrimidines. Their fungicidal activity was evaluated against the plant pathogens Puccinia recondita Rob. ex Desm. f. sp. tritici (Eriks.) CO Johnston (wheat brown rust), Mycosphaerella graminicola (Fuckel) Schroter (Septoria tritici Rob., leaf spot of wheat) and Magnaporthe grisea (Hebert) Barr (Pyricularia oryzae Cav., rice blast). Structure-activity relationship studies revealed the advantage of a fluoro substituent in position 6 and of a secondary amine in position 8. CONCLUSION: 8-Amino-7-aryl-6-halogen-substituted pyrido[2,3-b]pyrazines have been prepared as 6,6-biheterocyclic analogues of similarly substituted triazolopyrimidine fungicides. A concise four-step synthesis route has been worked out to prepare these novel compounds from commercially available starting materials. [(R)-(1,2-Dimethylpropyl)]-[6-fluoro-7-(2,4,6-trifluorophenyl)pyrido[2,3-b]pyrazin-8-yl]amine showed excellent activity against three economically important phytopathogens.
Subject(s)
Fungicides, Industrial/chemical synthesis , Fungicides, Industrial/pharmacology , Pyrazines/chemical synthesis , Pyrazines/pharmacology , Tubulin Modulators/chemical synthesis , Tubulin Modulators/pharmacology , Fungi/drug effects , Fungicides, Industrial/chemistry , Plant Diseases/microbiology , Pyrazines/chemistry , Structure-Activity Relationship , Triticum/microbiology , Tubulin Modulators/chemistryABSTRACT
A review, outlining the origins and subsequent development of the triketone class of herbicidal 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitors.
Subject(s)
4-Hydroxyphenylpyruvate Dioxygenase/antagonists & inhibitors , Enzyme Inhibitors/chemistry , Herbicides/chemistry , Ketones/chemistry , 4-Hydroxyphenylpyruvate Dioxygenase/metabolism , Enzyme Inhibitors/chemical synthesis , Enzyme Inhibitors/pharmacology , Herbicides/chemical synthesis , Herbicides/pharmacology , Ketones/chemical synthesis , Ketones/pharmacology , Structure-Activity RelationshipABSTRACT
The preparation of the C1-C11 subunit of phoslactomycins, and a formal synthesis of phoslactomycin B, were achieved by a convergent strategy involving the chelation-controlled addition of an alkynyl Grignard reagent to an alpha-alkoxy ketone. Catalytic enantioselective reductions of acetylenic ketones and a [2,3]-Wittig rearrangement were utilized as key steps to control the configuration of the C4, C5, and C9 stereocenters.
Subject(s)
Catalysis , Copper/chemistry , Epoxy Compounds/chemical synthesis , Epoxy Compounds/chemistry , Indicators and Reagents , Ketones/chemical synthesis , Ketones/chemistry , Lactones/chemical synthesis , Lactones/chemistry , Molecular Structure , Organophosphorus Compounds/chemical synthesis , Organophosphorus Compounds/chemistry , StereoisomerismABSTRACT
Alkynylalanes provide a new, copper-free route to skipped diynes when combined with propargylic electrophiles bearing an aluminum-complexing leaving group. The reaction is mild, efficient, and, in contrast to copper-mediated methods, highly regioselective. [reaction: see text]
ABSTRACT
[reaction: see text] We have developed a novel reaction between a terminal TMS-alkyne and a propargyl halide in the presence of a fluoride source and a catalytic amount of copper iodide to prepare 1,4-skipped diynes with good yields and in mild conditions. We have shown that this reaction also works very well with germanium and tin derivatives as an alternative to silicon. This new method can be useful for the synthesis of polyunsaturated fatty acids.
ABSTRACT
Thermodynamic and structural properties of a chemically modified DNA-RNA hybrid in which a phosphodiester linkage is replaced by a neutral amide-3 linkage (3'-CH(2)-CONH-5') were investigated using UV melting experiments, molecular dynamics simulations in explicit water, and continuum solvent models. van't Hoff analysis of the experimental UV melting curves suggests that the significant increase of the thermodynamic stability of a 15-mer DNA-RNA with seven alternated amide-3 modifications (+11 degrees C) is mainly due to an increased binding enthalpy. To further evaluate the origin in the observed affinities differences, the electrostatic contribution to the binding free energy was calculated by solving the Poisson-Boltzmann equation numerically. The nonelectrostatic contribution was estimated as the product of a hydrophobic surface tension coefficient and the surface area that is buried upon double strand formation. Structures were taken from 10 ns molecular dynamics simulations computed in a consistent fashion using explicit solvent, counterions, and the particle-mesh Ewald procedure. The present preliminary thermodynamic study suggests that the favorable binding free energy of the amide-3 DNA single strand to the complementary RNA is equally driven by electrostatic and nonpolar contributions to the binding compared to their natural analogues. In addition, molecular dynamics simulations in explicit water were performed on an amide-3 DNA single strand and the corresponding natural DNA. Results from the conformations cluster analysis of the simulated amide-3 DNA single strand ensembles suggest that the 25% of the population sampled within 10 ns has a pre-organized conformation where the sugar C3' endo pucker is favored at the 3'-flanking nucleotides. These structural and thermodynamic features contribute to the understanding of the observed increased affinities of the amide-3 DNA-RNA hybrids at the microscopic level.