Inflammatory bowel diseases(IBDs)comprising ulcerative colitis,Crohn’s disease and microscopic colitis are characterized by chronic inflammation of the gastrointestinal tract.IBD has spread around the world and is be...Inflammatory bowel diseases(IBDs)comprising ulcerative colitis,Crohn’s disease and microscopic colitis are characterized by chronic inflammation of the gastrointestinal tract.IBD has spread around the world and is becoming more prevalent at an alarming rate in developing countries whose societies have become more westernized.Cell therapy,intestinal microecology,apheresis therapy,exosome therapy and small molecules are emerging therapeutic options for IBD.Currently,it is thought that low-molecular-mass substances with good oral bio-availability and the ability to permeate the cell membrane to regulate the action of elements of the inflammatory signaling pathway are effective therapeutic options for the treatment of IBD.Several small molecule inhibitors are being developed as a promising alternative for IBD therapy.The use of highly efficient and time-saving techniques,such as computational methods,is still a viable option for the development of these small molecule drugs.The computeraided(in silico)discovery approach is one drug development technique that has mostly proven efficacy.Computational approaches when combined with traditional drug development methodology dramatically boost the likelihood of drug discovery in a sustainable and cost-effective manner.This review focuses on the modern drug discovery approaches for the design of novel IBD drugs with an emphasis on the role of computational methods.Some computational approaches to IBD genomic studies,target identification,and virtual screening for the discovery of new drugs and in the repurposing of existing drugs are discussed.展开更多
With the goal of suggesting dual inhibitors of HIV reverse transcriptase (RT) and integrase (IN), herein we report the molecular docking of an initial set of 556 compounds related to the pyridinone class. Docking with...With the goal of suggesting dual inhibitors of HIV reverse transcriptase (RT) and integrase (IN), herein we report the molecular docking of an initial set of 556 compounds related to the pyridinone class. Docking with multiple crystallographic structures of HIV-1 RT led to 160 potential binders of RT interacting with key amino acid residues at the enzyme’s allosteric site. Compounds selected from the docking with RT were further docked with a crystallographic structure of HIV-1 IN. A total of 31 structures had the potential to make contacts with Mg2+ ions located in a small space between DNA and IN. Interactions with Mg2+ ions are relevant because they participate in the stabilization of the IN-DNA complex. In conclusion, 31 compounds synthetically accessible are proposed as dual inhibitors of RT and IN. It is hypothesized that the suggested compounds will inhibit RT by occupying the allosteric site for NNRTIs and will inhibit the catalytic activity of IN by destabilizing the IN-DNA complex. The main perspective of this work is the synthesis and biological testing of the candidate molecules.展开更多
Based on the concept of Green Chemistry, a new procedure of finding bioactive compounds and their synthetic routes by computer-aided techniques was proposed. The procedure consists of pharmacopoeia search against a 3D...Based on the concept of Green Chemistry, a new procedure of finding bioactive compounds and their synthetic routes by computer-aided techniques was proposed. The procedure consists of pharmacopoeia search against a 3D structural database of natural products for lead discovery and computer-aided synthesis design for avoiding un useful synthetic experiments. This work demonstrated that computer aided drug design and synthesis design would help us to make the consideration of environmental concerns systematically, rather than having to deal later with the unnecessary waste chemicals. Thus, it is shown that chemical computer-aided design (CAD) is an indispensable part of Green Chemistry.展开更多
甲状旁腺素能增加人体骨密度和骨强度,是治疗骨质疏松症最有效的多肽类药物之一,但至今缺乏具有相应功能的小分子药物。根据计算机辅助药物设计原理,采用Discovery Studio 2.5软件包,以14个甲状旁腺素(PTH)受体激动剂及其突变类似物为...甲状旁腺素能增加人体骨密度和骨强度,是治疗骨质疏松症最有效的多肽类药物之一,但至今缺乏具有相应功能的小分子药物。根据计算机辅助药物设计原理,采用Discovery Studio 2.5软件包,以14个甲状旁腺素(PTH)受体激动剂及其突变类似物为训练集,利用活性构象限制的方法,采用HypoGen算法构建出具有活性预测功能的3D药效团模型。其中最好的药效团模型含有1个阳离子基团(PI),3个疏水中心(H)和1个氢键供体(HBD)。同时应用该模型成功预测出16个测试集分子的活性,经交叉验证表明该模型达到95%的置信水平,具有良好的活性预测能力。该药效团可以用于后续抗骨质疏松症小分子药物的筛选,指导相应的药物优化,同时所采用的限制构象的药效团生产方法为基于多肽的药物设计提供了一个新的思路。展开更多
Integrase has become an attractive target for the design of anti-HIV inhibitor because it plays a quite important role in the process of HIV-1 virus replication. The quinoline ring derivatives, which have the similar ...Integrase has become an attractive target for the design of anti-HIV inhibitor because it plays a quite important role in the process of HIV-1 virus replication. The quinoline ring derivatives, which have the similar pharmacophore toβ-diketoacids, are the kind of integrase inhibitor with highly antiviral activity. A series of quinoline ring derivatives were analyzed by the comparative molecular field analysis(Co MFA), comparative molecular similarity induces analysis(Co MSIA) and Topomer Co MFA methods. Firstly, we chose 77 compounds from former papers as a dataset,followed by dividing it into the training set and test set randomly. Then, we constructed predictive models of Co MFA, Co MSIA and Topomer Co MFA, respectively. The Co MFA yielded the best cross-validated model with a q2=0.758, non-cross-validated r2=0.988.The Co MSIA model yielded a q2=0.701 and r2=0.986 while the Topomer Co MFA model has q2=0.661 and r2=0.966. Through verification, these results suggested a strong predictive ability to the design of novel highly active HIV-1 integrase inhibitors for therapy.展开更多
文摘Inflammatory bowel diseases(IBDs)comprising ulcerative colitis,Crohn’s disease and microscopic colitis are characterized by chronic inflammation of the gastrointestinal tract.IBD has spread around the world and is becoming more prevalent at an alarming rate in developing countries whose societies have become more westernized.Cell therapy,intestinal microecology,apheresis therapy,exosome therapy and small molecules are emerging therapeutic options for IBD.Currently,it is thought that low-molecular-mass substances with good oral bio-availability and the ability to permeate the cell membrane to regulate the action of elements of the inflammatory signaling pathway are effective therapeutic options for the treatment of IBD.Several small molecule inhibitors are being developed as a promising alternative for IBD therapy.The use of highly efficient and time-saving techniques,such as computational methods,is still a viable option for the development of these small molecule drugs.The computeraided(in silico)discovery approach is one drug development technique that has mostly proven efficacy.Computational approaches when combined with traditional drug development methodology dramatically boost the likelihood of drug discovery in a sustainable and cost-effective manner.This review focuses on the modern drug discovery approaches for the design of novel IBD drugs with an emphasis on the role of computational methods.Some computational approaches to IBD genomic studies,target identification,and virtual screening for the discovery of new drugs and in the repurposing of existing drugs are discussed.
文摘With the goal of suggesting dual inhibitors of HIV reverse transcriptase (RT) and integrase (IN), herein we report the molecular docking of an initial set of 556 compounds related to the pyridinone class. Docking with multiple crystallographic structures of HIV-1 RT led to 160 potential binders of RT interacting with key amino acid residues at the enzyme’s allosteric site. Compounds selected from the docking with RT were further docked with a crystallographic structure of HIV-1 IN. A total of 31 structures had the potential to make contacts with Mg2+ ions located in a small space between DNA and IN. Interactions with Mg2+ ions are relevant because they participate in the stabilization of the IN-DNA complex. In conclusion, 31 compounds synthetically accessible are proposed as dual inhibitors of RT and IN. It is hypothesized that the suggested compounds will inhibit RT by occupying the allosteric site for NNRTIs and will inhibit the catalytic activity of IN by destabilizing the IN-DNA complex. The main perspective of this work is the synthesis and biological testing of the candidate molecules.
基金Special article from the First International workshop on Green Chemistry, the University of ScienceTechnology of China, Hefei, China, May, 1998.Project supported in part by grants from the State Plan Commission of China (No. 96-547-01), the National
文摘Based on the concept of Green Chemistry, a new procedure of finding bioactive compounds and their synthetic routes by computer-aided techniques was proposed. The procedure consists of pharmacopoeia search against a 3D structural database of natural products for lead discovery and computer-aided synthesis design for avoiding un useful synthetic experiments. This work demonstrated that computer aided drug design and synthesis design would help us to make the consideration of environmental concerns systematically, rather than having to deal later with the unnecessary waste chemicals. Thus, it is shown that chemical computer-aided design (CAD) is an indispensable part of Green Chemistry.
文摘甲状旁腺素能增加人体骨密度和骨强度,是治疗骨质疏松症最有效的多肽类药物之一,但至今缺乏具有相应功能的小分子药物。根据计算机辅助药物设计原理,采用Discovery Studio 2.5软件包,以14个甲状旁腺素(PTH)受体激动剂及其突变类似物为训练集,利用活性构象限制的方法,采用HypoGen算法构建出具有活性预测功能的3D药效团模型。其中最好的药效团模型含有1个阳离子基团(PI),3个疏水中心(H)和1个氢键供体(HBD)。同时应用该模型成功预测出16个测试集分子的活性,经交叉验证表明该模型达到95%的置信水平,具有良好的活性预测能力。该药效团可以用于后续抗骨质疏松症小分子药物的筛选,指导相应的药物优化,同时所采用的限制构象的药效团生产方法为基于多肽的药物设计提供了一个新的思路。
文摘Integrase has become an attractive target for the design of anti-HIV inhibitor because it plays a quite important role in the process of HIV-1 virus replication. The quinoline ring derivatives, which have the similar pharmacophore toβ-diketoacids, are the kind of integrase inhibitor with highly antiviral activity. A series of quinoline ring derivatives were analyzed by the comparative molecular field analysis(Co MFA), comparative molecular similarity induces analysis(Co MSIA) and Topomer Co MFA methods. Firstly, we chose 77 compounds from former papers as a dataset,followed by dividing it into the training set and test set randomly. Then, we constructed predictive models of Co MFA, Co MSIA and Topomer Co MFA, respectively. The Co MFA yielded the best cross-validated model with a q2=0.758, non-cross-validated r2=0.988.The Co MSIA model yielded a q2=0.701 and r2=0.986 while the Topomer Co MFA model has q2=0.661 and r2=0.966. Through verification, these results suggested a strong predictive ability to the design of novel highly active HIV-1 integrase inhibitors for therapy.
