Small-molecule drugs are essential for maintaining human health. The objective of this study is to identify a molecule that can inhibit the Factor Xa protein and be easily procured. An optimization-based de novo drug ...Small-molecule drugs are essential for maintaining human health. The objective of this study is to identify a molecule that can inhibit the Factor Xa protein and be easily procured. An optimization-based de novo drug design framework, Drug CAMD, that integrates a deep learning model with a mixed-integer nonlinear programming model is used for designing drug candidates. Within this framework, a virtual chemical library is specifically tailored to inhibit Factor Xa. To further filter and narrow down the lead compounds from the designed compounds, comprehensive approaches involving molecular docking,binding pose metadynamics(BPMD), binding free energy calculations, and enzyme activity inhibition analysis are utilized. To maximize efficiency in terms of time and resources, molecules for in vitro activity testing are initially selected from commercially available portions of customized virtual chemical libraries. In vitro studies assessing inhibitor activities have confirmed that the compound EN300-331859shows potential Factor Xa inhibition, with an IC_(50)value of 34.57 μmol·L^(-1). Through in silico molecular docking and BPMD, the most plausible binding pose for the EN300-331859-Factor Xa complex are identified. The estimated binding free energy values correlate well with the results obtained from biological assays. Consequently, EN300-331859 is identified as a novel and effective sub-micromolar inhibitor of Factor Xa.展开更多
The zebra mussel is an important aquatic pest that causes great damage to freshwater-dependent industries, due to biofouling. The main goal of the project discussed here is to develop improved solutions to control thi...The zebra mussel is an important aquatic pest that causes great damage to freshwater-dependent industries, due to biofouling. The main goal of the project discussed here is to develop improved solutions to control this species. Three approaches have been explored in an attempt to design innovative application strategies for existing biocides： （i） encapsulation of toxins; （ii） combination of toxins; （iii） investigation of the seasonal variation of the species＇ tolerance to toxins. In this paper, the principles behind these approaches and the major results on each topic are presented. The benefits of adopting a chemical product engineering approach in conducting this project are also discussed.展开更多
基金financial supports of the National Natural Science Foundation of China (22078041, 22278053,22208042)Dalian High-level Talents Innovation Support Program (2023RQ059)“the Fundamental Research Funds for the Central Universities (DUT20JC41, DUT22YG218)”。
文摘Small-molecule drugs are essential for maintaining human health. The objective of this study is to identify a molecule that can inhibit the Factor Xa protein and be easily procured. An optimization-based de novo drug design framework, Drug CAMD, that integrates a deep learning model with a mixed-integer nonlinear programming model is used for designing drug candidates. Within this framework, a virtual chemical library is specifically tailored to inhibit Factor Xa. To further filter and narrow down the lead compounds from the designed compounds, comprehensive approaches involving molecular docking,binding pose metadynamics(BPMD), binding free energy calculations, and enzyme activity inhibition analysis are utilized. To maximize efficiency in terms of time and resources, molecules for in vitro activity testing are initially selected from commercially available portions of customized virtual chemical libraries. In vitro studies assessing inhibitor activities have confirmed that the compound EN300-331859shows potential Factor Xa inhibition, with an IC_(50)value of 34.57 μmol·L^(-1). Through in silico molecular docking and BPMD, the most plausible binding pose for the EN300-331859-Factor Xa complex are identified. The estimated binding free energy values correlate well with the results obtained from biological assays. Consequently, EN300-331859 is identified as a novel and effective sub-micromolar inhibitor of Factor Xa.
基金the Portuguese Foundation for Science and Technology (scholarship SFRH/BD/18731/2004 and Research Project Grant POCI/EQU/59305/2004).
文摘The zebra mussel is an important aquatic pest that causes great damage to freshwater-dependent industries, due to biofouling. The main goal of the project discussed here is to develop improved solutions to control this species. Three approaches have been explored in an attempt to design innovative application strategies for existing biocides： （i） encapsulation of toxins; （ii） combination of toxins; （iii） investigation of the seasonal variation of the species＇ tolerance to toxins. In this paper, the principles behind these approaches and the major results on each topic are presented. The benefits of adopting a chemical product engineering approach in conducting this project are also discussed.
