Molecular dynamics was used to simulate the transition state for the first chemical reaction step (TS1) of cocaine hydrolysis catalyzed by human butyrylcholinesterase (BChE) and its mutants. The simulated results demonstrate that the overall hydrogen bonding between the carbonyl oxygen of (؊)-cocaine benzoyl ester and the oxyanion hole of BChE in the TS1 structure for (؊)-cocaine hydrolysis catalyzed by A199S͞S287G͞A328W͞Y332G BChE should be significantly stronger than that in the TS1 structure for (؊)-cocaine hydrolysis catalyzed by the WT BChE and other simulated BChE mutants. Thus, the transition-state simulations predict that A199S͞ S287G͞A328W͞Y332G mutant of BChE should have a significantly lower energy barrier for the reaction process and, therefore, a significantly higher catalytic efficiency for (؊)-cocaine hydrolysis. The theoretical prediction has been confirmed by wet experimental tests showing an Ϸ(456 ؎ 41)-fold improved catalytic efficiency of A199S͞S287G͞A328W͞Y332G BChE against (؊)-cocaine. This is a unique study to design an enzyme mutant based on transitionstate simulation. The designed BChE mutant has the highest catalytic efficiency against cocaine of all of the reported BChE mutants, demonstrating that the unique design approach based on transition-state simulation is promising for rational enzyme redesign and drug discovery. molecular dynamics ͉ rational design ͉ transition-state stabilization ͉ cocaine ͉ enzyme-substrate binding C ocaine is recognized as the most reinforcing of all drugs of abuse (1-3). The disastrous medical and social consequences of cocaine addiction have made the development of an effective pharmacological treatment a high priority (4-6). However, cocaine mediates its reinforcing and toxic effects by blocking neurotransmitter reuptake, and the classical pharmacodynamic approach has failed to yield small-molecule receptor antagonists because of the difficulties inherent in blocking a blocker (1-5). An alternative to receptor-based approaches is to interfere with the delivery of cocaine to its receptors or accelerate its metabolism in the body (5,(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17). An ideal molecule for this purpose should be a potent enzyme catalyzing the hydrolysis of cocaine into biologically inactive metabolites. The dominant pathway for cocaine metabolism in primates is butyrylcholinesterase (BChE)-catalyzed hydrolysis at the benzoyl ester group (Fig. 3, which is published as supporting information on the PNAS web site), and the metabolites are all biologically inactive (5, 18). Clearly, BChE-catalyzed hydrolysis of cocaine at the benzoyl ester is the metabolic pathway most suitable for amplification. However, the catalytic activity of this plasma enzyme is Ϸ1,000-fold lower against the naturally occurring (Ϫ)-cocaine than that against the biologically inactive (ϩ)-cocaine enantiomer (19)(20)(21)(22). (ϩ)-cocaine can be cleared from plasma in seconds, before partitioning into the CNS, whereas (Ϫ)-cocaine has a plasma half-life of Ϸ45-90 min, long enough for ...

Pd-catalyzed cross-coupling reactions have become essential tools for the construction of carbon-carbon and carbon-heteroatom bonds. Over the last three decades, great efforts have been made with cross-coupling chemistry in the discovery, development, and commercialization of innovative new pharmaceuticals and agrochemicals (mainly herbicides, fungicides, and insecticides). In view of the growing interest in both modern crop protection and cross-coupling chemistry, this review gives a comprehensive overview of the successful applications of various Pd-catalyzed cross-coupling methodologies, which have been implemented as key steps in the synthesis of agrochemicals (on R&D and pilot-plant scales) such as the Heck, Suzuki, Sonogashira, Stille, and Negishi reactions, as well as decarboxylative, carbonylative, α-arylative, and carbon-nitrogen bond bond-forming cross-coupling reactions. Some perspectives and challenges for these catalytic coupling processes in the discovery of agrochemicals are briefly discussed in the final section. The examples chosen demonstrate that cross-coupling chemistry approaches open-up new, low-cost, and more efficient industrial routes to existing agrochemicals, and such methods also have the capability to lead the new generation of pesticides with novel modes of action for sustainable crop protection.

Modern agricultural chemistry has to support farmers by providing innovative agrochemicals. In this context, the introduction of sulfur atoms into an active ingredient is still an important tool in modulating the properties of new crop-protection compounds. More than 30% of today's agrochemicals contain at least one sulfur atom, mainly in fungicides, herbicides and insecticides. A number of recently developed sulfur-containing agrochemical candidates represent a novel class of chemical compounds with new modes of action, so we intend to highlight the emerging interest in commercially active sulfur-containing compounds. This chapter gives a comprehensive overview of selected leading sulfur-containing pesticidal chemical families namely: sulfonylureas, sulfonamides, sulfur-containing heterocyclics, thioureas, sulfides, sulfones, sulfoxides and sulfoximines. Also, the most suitable large-scale synthetic methods of the recently launched or provisionally approved sulfur-containing agrochemicals from respective chemical families have been highlighted.

A series of diphenyl ether-containing pyrazole-carboxamide derivatives was designed and synthesized as new succinate ubiquinone oxidoreductase (SQR) inhibitors. This highly potent molecular scaffold was developed from a moderately activie hit 3, obtained from our previous pharmacophore-linked fragment virtual screening (PFVS) method. The results of greenhouse tests indicated that some analogues showed good SQR inhibitory activity, with promising fungicidal activity against Rhizoctonia solani and Sphaerotheca fuliginea at a dosage of 200 mg/L. Most surprisingly, compound 62 showed the highest SQR inhibitory activity with a K value of 0.081 μM, about 4-fold more potent than penthiopyrad (K = 0.307 μM). In addition, compounds 43 and 62 displayed excellent fungicidal activity even at a dosage as low as 6.25 mg/L, which was superior to thifluzamide. Moreover, compound 62 exhibited excellent protection effect against R. solani and provided about 81.2% protective control efficancy after 21 days with two sprayings. The present work indicated that these two compounds could be used as potential agricultural fungicides targeting SQR.

Slow‐binding inhibitors with long residence time on the target often display superior efficacy in vivo. Rationally designing inhibitors with low off‐target rates is restricted by a limited understanding of the structural basis of slow‐binding inhibition kinetics in enzyme–drug interactions. 4‐Hydroxyphenylpyruvate dioxygenase (HPPD) is an important target for drug and herbicide development. Although the time‐dependent behavior of HPPD inhibitors has been studied for decades, its structural basis and mechanism remain unclear. Herein, we report a detailed experimental and computational study that explores structures for illustrating the slow‐binding inhibition kinetics of HPPD. We observed the conformational change of Phe428 at the C‐terminal α‐helix in the inhibitor‐bound structures and further identified that the inhibition kinetics of drugs are related to steric hindrance of Phe428. These detailed structural and mechanistic insights illustrate that steric hindrance is highly associated with the time‐dependent behavior of HPPD inhibitors. These findings may enable rational design of new potent HPPD‐targeted drugs or herbicides with longer target residence time and improved properties. Database Structure data are available in the PDB under the accession numbers (released), (released), and (released).

A critical challenge to the fragment-based drug discovery (FBDD) is its low-throughput nature due to the necessity of biophysical method-based fragment screening. Herein, a method of pharmacophore-linked fragment virtual screening (PFVS) was successfully developed. Its application yielded the first picomolar-range Q(o) site inhibitors of the cytochrome bc(1) complex, an important membrane protein for drug and fungicide discovery. Compared with the original hit compound 4 (K(i) = 881.80 nM, porcine bc(1)), the most potent compound 4f displayed 20 507-fold improved binding affinity (K(i) = 43.00 pM). Compound 4f was proved to be a noncompetitive inhibitor with respect to the substrate cytochrome c, but a competitive inhibitor with respect to the substrate ubiquinol. Additionally, we determined the crystal structure of compound 4e (K(i) = 83.00 pM) bound to the chicken bc(1) at 2.70 Å resolution, providing a molecular basis for understanding its ultrapotency. To our knowledge, this study is the first application of the FBDD method in the discovery of picomolar inhibitors of a membrane protein. This work demonstrates that the novel PFVS approach is a high-throughput drug discovery method, independent of biophysical screening techniques.

4-Hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27, HPPD) is an important target for new bleaching herbicides discovery. As a continuous work to discover novel crop selective HPPD inhibitor, a series of 2-(aryloxyacetyl)cyclohexane-1,3-diones were rationally designed and synthesized by an efficient one-pot procedure using N,N'-carbonyldiimidazole (CDI), triethylamine, and acetone cyanohydrin in CHCl. A total of 58 triketone compounds were synthesized in good to excellent yields. Some of the triketones displayed potent in vitro Arabidopsis thaliana HPPD (AtHPPD) inhibitory activity. 2-(2-((1-Bromonaphthalen-2-yl)oxy)acetyl)-3-hydroxycyclohex-2-en-1-one, II-13, displayed high, broad-spectrum, and postemergent herbicidal activity at the dosage of 37.5-150 g ai/ha, nearly as potent as mesotrione against some weeds. Furthermore, II-13 showed good crop safety against maize and canola at the rate of 150 g ai/ha, indicating that II-13 might have potential as a herbicide for weed control in maize and canola fields. II-13 is the first HPPD inhibitor showing good crop safety toward canola.

The concept of drug-likeness has been established in the field of drug discovery. Pesticide discovery is also a complicated and rigorous filtering process compared with drug discovery. This study involved investigation of the constitutive properties of 788 marketed pesticides, including 341 herbicides, 182 fungicides, and 265 insecticides. In a comparison of the constitutive properties of different kinds of pesticides and of pesticides from different periods of registration, ClogP, the number of H-bond donors (HBD), and the number of aromatic bonds (ARB) were identified as the most important factors that distinguish herbicides, fungicides, and insecticides. In addition, the reduction in pesticide toxicity with revolution time was found to have some relationship with an increase in values of the six constitutive properties. Finally, we established some rules for pesticide-likeness, including molecular weight≤435 Da, ClogP≤6, number of H-bond acceptors (HBA)≤6, HBD≤2, number of rotatable bonds (ROB)≤9, and ARB≤17. The constitutive property-related novel findings in this study will promote the structure-based optimization of pesticide candidates.