Modern computational chemistry has reached a stage at which massive exploration into chemical reaction space with unprecedented resolution with respect to the number of potentially relevant molecular structures has become possible. Various algorithmic advances have shown that such structural screenings must and can be automated and routinely carried out. This will replace the standard approach of manually studying a selected and restricted number of molecular structures for a chemical mechanism. The complexity of the task has led to many different approaches. However, all of them address the same general target, namely to produce a complete atomistic picture of the kinetics of a chemical process. It is the purpose of this overview to categorize the problems that should be targeted and to identify the principal components and challenges of automated exploration machines so that the various existing approaches and future developments can be compared based on well-defined conceptual principles.
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http://dx.doi.org/10.1146/annurev-physchem-071119-040123 | DOI Listing |
Chaos
January 2025
Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
Spirals are a special class of excitable waves that have its significance in the understanding of cardiac arrests and neuronal transduction. In a theoretical model of the chemical Belousov-Zhabotinsky reaction system, we explore the dynamics of the spatiotemporal patterns that emerge out of competing reaction and diffusion phenomena. By modifying the existing mathematical models of the reaction kinetics, we have been able to explore the explicit effect of hydrogen ion concentration in the system, so as to achieve various regimes of wave activity, from stable spirals to oscillation death.
View Article and Find Full Text PDFJ Med Chem
January 2025
Pharmaron Beijing Co., Ltd., 6 Taihe Road, BDA, Beijing 100176, P. R. China.
Despite recent advances in the inhibition of EGFR (epidermal growth factor receptor), there remains a clinical need for new EGFR Exon20 insertion (Ex20Ins) inhibitors that spare EGFR WT. Herein, we report the discovery and optimization of two chemical series leading to ether and biaryl as potent, selective, and brain-penetrant inhibitors of Ex20Ins mutants. Building on our earlier discovery of alkyne which allowed access to CNS property space for an Ex20Ins inhibitor, we utilized structure-based design to move to lower lipophilicity and lower CL compounds while maintaining a WT selectivity margin.
View Article and Find Full Text PDFJ Am Chem Soc
January 2025
Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523-1872, United States.
Enthalpy is often the focal point when designing monomers for polymer circularity, but much less is explored on how entropy can be exploited to create polymers with synergistic circularity and properties. Here, we design a series of spiro-lactones (SLs) with closed-chain cycloalk(en)yl substituents at the α,α-position of δ-valerolactone (δVL), which, when combined with the parent δVL and -α,α-dialkyl-substituted δVL with open-chain alkyl groups, provide a desired platform for exploring the circular polymer design by focusing on the entropy change of polymerization. These SLs exhibit finely balanced (de)polymerizability that is regulated chiefly by entropy differentiation, allowing both the facile synthesis of polyester PSLs ( up to 1000 kg mol) in a living fashion and selective depolymerization of the PSLs to completely recover monomers under mild conditions (using a recyclable catalyst at 100 °C).
View Article and Find Full Text PDFPLoS One
January 2025
Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt.
This study presents T-1-NBAB, a new compound derived from the natural xanthine alkaloid theobromine, aimed at inhibiting VEGFR-2, a crucial protein in angiogenesis. T-1-NBAB's potential to interacts with and inhibit the VEGFR-2 was indicated using in silico techniques like molecular docking, MD simulations, MM-GBSA, PLIP, essential dynamics, and bi-dimensional projection experiments. DFT experiments was utilized also to study the structural and electrostatic properties of T-1-NBAB.
View Article and Find Full Text PDFMicrob Biotechnol
January 2025
Laboratory of Microbiology, Institute of Biology, University of Neuchatel, Neuchatel, Switzerland.
The inadequate removal of pharmaceuticals and personal care products (PPCPs) by traditional wastewater treatment plants (WWTPs) poses a significant environmental and public health challenge. Residual PPCPs find their way into aquatic ecosystems, leading to bioaccumulation in aquatic biota, the dissemination of antibiotic resistance genes (ARGs), and contamination of both water sources and vegetables. These persistent pollutants can have negative effects on human health, ranging from antibiotic resistance development to endocrine disruption.
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