Diabetes is a serious, long-term (or chronic) disease that occurs when a person’s blood sugar levels are high because their body cannot produce enough insulin, or does not produce enough insulin or that it cannot eff...Diabetes is a serious, long-term (or chronic) disease that occurs when a person’s blood sugar levels are high because their body cannot produce enough insulin, or does not produce enough insulin or that it cannot effectively use the insulin it produces. According to the literature, this disease has several causes, but certain types of diabetes such as type 2 diabetes are most closely linked to a metabolic disorder due to abdominal obesity. Thus, the number of individuals with type 2 diabetes is increasing. It is with this in mind that we work to improve human health. The aim of this study is to design new derivatives of 1,3,4-thiadiazole with improved antidiabetic activity by the mathematical model of multiple linear regression (MLR) established previously. The analysis of the effect on the substituents influencing the antidiabetic activity, fourteen (14) new molecules coded CDTH were generated and presenting values of the potential of inhibitory concentration higher than that of the base compound (pIC50 = 2.526). But thirteen (13) of these new compounds belong to the domain of applicability of the MLR model established previously. In addition, the thermodynamic quantities of formation formed at 298K have been calculated. Lipinski’s rule and pharmacokinetic properties proved that five (5) (TH4, TH9, TH10, TH13 and TH14) new molecules can be used as diabetes medicine.展开更多
Traditional Chinese Medicine(TCM)is an important reservoir for bioactive natural products.TCM extraction methods by water decoction and wine tincture are an integral part of TCM and essential for their widely acknowle...Traditional Chinese Medicine(TCM)is an important reservoir for bioactive natural products.TCM extraction methods by water decoction and wine tincture are an integral part of TCM and essential for their widely acknowledged efficacy.In this study,we selected 6 common TCMs that are rich in chemistry to investigate whether the TCM extraction methods deliver molecules with drug-like physical chemical properties.Six TCM herbal materials were extracted by water,95%ethanol,and sequential hexane,d ichloromethane and methanol.The extracts were analyzed by HPLC and^1H NMR.Isolation on one of the extracts yielded 32 compounds,their physical chemical properties were analyzed by Instant JChem.Our results showed that ethanol extraction,which mimics TCM wine tincture,delivered compounds with physical chemical properties compliant to Lipinski’s rule of 5.展开更多
Despite the vigorous research and development, as of 2017, there is currently no widely available antimalarial vaccine. An effective, commercially available vaccine would be a huge game changer;however, it seems like ...Despite the vigorous research and development, as of 2017, there is currently no widely available antimalarial vaccine. An effective, commercially available vaccine would be a huge game changer;however, it seems like there is still a long way to go until that target is reached. Therefore, the purpose of this study was to use molecular docking technique to identify new inhibitors for a novel antimalarial target with the overall aim of finding hit compounds which could be further optimized to become potential drug candidates. The docking protocol AutoDockVina was used alongside the molecular visualisation software UCSF Chimera to dock 100 naphthoquinones (labelled TM1-100) and 66 aryl diketones (labelled TM101-166) with the chosen target, Plasmodium vivax N-myristoyltransferase (PvNMT). Each docking session yielded the best 9 binding modes between the ligand and target. The hydrogen bond interactions of all binding modes were analysed, and the top six target molecules (TM) were short listed as the possible hit compounds (TM40, TM65, TM66, TM81, TM94 and TM165). These compounds displayed more than six hydrogen bonds under 3 angstroms over the 9 binding modes. Using Lipinski’s rule of 5, the potential hit compounds were further analysed to determine the drug-likeness and all were found to obey the parameters. Following the same method used to dock the ligands, twelve FDA approved antimalarial drugs were also docked with PvNMT for comparison purposes. Apart from proguanil, the other eleven antimalarial drugs displayed fewer hydrogen bonds under 3 angstroms over the 9 binding modes compared to all six of the potential hit compounds. This study discovered six compounds which displayed stronger interactions with the target protein compared to majority of the FDA approved drugs. The results of this investigation gave us new molecules that could be further investigated for the designing of novel drug-like compounds for the treatment of Malaria.展开更多
Lipinski’s “Rule of Five” was introduced for predicting oral bioavailability to describe drug-like molecules. For the purpose of this research the rules were used to separate potential inhibitors of HIV-1 integrase...Lipinski’s “Rule of Five” was introduced for predicting oral bioavailability to describe drug-like molecules. For the purpose of this research the rules were used to separate potential inhibitors of HIV-1 integrase (1BIS.pdb) into two groups: drug-like and nondrug-like. If one of Lipinski’s “Rule of Five” was not followed the potential inhibitor was classified as nondrug-like. Thirty molecules were identified from the literature, twenty-four drug-like and six nondrug-like, that were docked into the active site of 1BIS.pdb (considered the non-mutated protein) and two mutant models, Y143R and N155H. These are two of the mutations that have led to increased resistance to HIV-1 integrase drugs such as raltegravir and elvitegravir. The computational software, ICM-Pro (Molsoft L.L.C.), was used to determine the estimated binding energy (EBE) of the drug/protein complex. It was found that the nondrug-like molecules generally had a more negative EBE, that is, tighter binding with 1BIS. pdb, though there were several exceptions in the drug-like group. With the protein mutant model Y143R, the majority of drug-like (58%) and nondrug-like molecules (67%) had tighter binding. However, for the mutant model N155H, there was the same percent (46%) of drug-like molecules with tighter binding with the mutant model as with 1BIS.pdb. The drug-like molecules were used when there was a ≥1 kcal/mole difference between 1BIS.pdb and either of the two mutant models to suggest a pharmacophore with structural characteristics for an HIV-1 integrase inhibitor.展开更多
An approach of using molinspiration calculations and molecular docking on PBPs （penicillin-binding proteins） and certain β-lactamases is employed to predict the molecular properties, bioactivity and resistance of n...An approach of using molinspiration calculations and molecular docking on PBPs （penicillin-binding proteins） and certain β-lactamases is employed to predict the molecular properties, bioactivity and resistance of newer and reference cephalosporins. The previously synthesized cephalosporins 1-8 and reference cephalosporins were subjected to extensive evaluations by calculating the molecular properties, drug-likeness scores on the bases of Lipinski＇s rule and bioactivity prediction using the method of molinspiration web-based software. The TPSA （topological polar surface area）, OH-NH interactions, n-violation and the molinspiration Log partition coefficient （miLogP） values were also calculated. The investigated cephalosporins were subjected to molecular docking study on PBPs （lpyy） and on β-lactamases produced by S. aureus, K. pneumonia, E. coil and P. auroginosa using 1-click-docking website. Molecular properties of 1-8 recorded higher ＂FPSA than cephalexin and were lower than the reference cephalosporins and do not fulfill the requirements for Lipinski＇s rule. Bioactivities of 1-8 were predicted to be less and their docking scores on PBPs were comparable to those of the reference cephalosporins, particularly ceftobiprole. The references recorded various docking scores on the above β-lactamases and as expected, cefiobiprole recorded the lowest scores on all β-lactarnases. Cephalosporins 1-8 recorded various docking scores on β-lactamases. Molecular docking studies on PBPs and β-lactamases are considered as very useful, reliable and practical approach for predicting the bioactivity scores and to afford some information about the stability and selectivity of the newly proposed cephalosporins against β-lactamases of certain pathogenic microbes, such as P. auroginosa and MRSA, by recording the relative docking scores in comparison with those of reference cephalosporins.展开更多
目的优选抗HIV中药复方,通过复方小分子数据库的构建和类药性分析,为复方抗HIV活性分子研究奠定数据库基础。方法查阅文献和国内专利搜集抗HIV中药复方,优选复方确定研究对象,在中药系统药理学数据库和分析平台(traditional chinese med...目的优选抗HIV中药复方,通过复方小分子数据库的构建和类药性分析,为复方抗HIV活性分子研究奠定数据库基础。方法查阅文献和国内专利搜集抗HIV中药复方,优选复方确定研究对象,在中药系统药理学数据库和分析平台(traditional chinese medicine systems pharmacology database and analysis platform,TCMSP)分别下载该复方单味中药化学成分,构建复方小分子数据库,并基于"Lipinski规则"进行类药性分析。结果检索得到48个抗HIV复方,其中单味中药组成明确的复方有11个,优选双黄连粉针剂为研究对象,构建双黄连粉针剂复方小分子数据库,命名为SHLMD,包括481个化合物,包含萜类(121个)、黄酮类(61个)、苯丙素类(31个)和有机酸及其酯类(23个)等11类化合物,以萜类和黄酮类化合物居多。基于"Lipinski规则"筛选得到323个化合物,组成的新数据库命名为Lipinski-SHLMD。结论双黄连粉针剂是适合优先展开研究的抗HIV中药复方,构建的SHLMD为双黄连粉针剂的分子研究奠定了数据库基础,利用"Lipinski规则"初筛突出了研究重点。展开更多
文摘Diabetes is a serious, long-term (or chronic) disease that occurs when a person’s blood sugar levels are high because their body cannot produce enough insulin, or does not produce enough insulin or that it cannot effectively use the insulin it produces. According to the literature, this disease has several causes, but certain types of diabetes such as type 2 diabetes are most closely linked to a metabolic disorder due to abdominal obesity. Thus, the number of individuals with type 2 diabetes is increasing. It is with this in mind that we work to improve human health. The aim of this study is to design new derivatives of 1,3,4-thiadiazole with improved antidiabetic activity by the mathematical model of multiple linear regression (MLR) established previously. The analysis of the effect on the substituents influencing the antidiabetic activity, fourteen (14) new molecules coded CDTH were generated and presenting values of the potential of inhibitory concentration higher than that of the base compound (pIC50 = 2.526). But thirteen (13) of these new compounds belong to the domain of applicability of the MLR model established previously. In addition, the thermodynamic quantities of formation formed at 298K have been calculated. Lipinski’s rule and pharmacokinetic properties proved that five (5) (TH4, TH9, TH10, TH13 and TH14) new molecules can be used as diabetes medicine.
文摘Traditional Chinese Medicine(TCM)is an important reservoir for bioactive natural products.TCM extraction methods by water decoction and wine tincture are an integral part of TCM and essential for their widely acknowledged efficacy.In this study,we selected 6 common TCMs that are rich in chemistry to investigate whether the TCM extraction methods deliver molecules with drug-like physical chemical properties.Six TCM herbal materials were extracted by water,95%ethanol,and sequential hexane,d ichloromethane and methanol.The extracts were analyzed by HPLC and^1H NMR.Isolation on one of the extracts yielded 32 compounds,their physical chemical properties were analyzed by Instant JChem.Our results showed that ethanol extraction,which mimics TCM wine tincture,delivered compounds with physical chemical properties compliant to Lipinski’s rule of 5.
文摘Despite the vigorous research and development, as of 2017, there is currently no widely available antimalarial vaccine. An effective, commercially available vaccine would be a huge game changer;however, it seems like there is still a long way to go until that target is reached. Therefore, the purpose of this study was to use molecular docking technique to identify new inhibitors for a novel antimalarial target with the overall aim of finding hit compounds which could be further optimized to become potential drug candidates. The docking protocol AutoDockVina was used alongside the molecular visualisation software UCSF Chimera to dock 100 naphthoquinones (labelled TM1-100) and 66 aryl diketones (labelled TM101-166) with the chosen target, Plasmodium vivax N-myristoyltransferase (PvNMT). Each docking session yielded the best 9 binding modes between the ligand and target. The hydrogen bond interactions of all binding modes were analysed, and the top six target molecules (TM) were short listed as the possible hit compounds (TM40, TM65, TM66, TM81, TM94 and TM165). These compounds displayed more than six hydrogen bonds under 3 angstroms over the 9 binding modes. Using Lipinski’s rule of 5, the potential hit compounds were further analysed to determine the drug-likeness and all were found to obey the parameters. Following the same method used to dock the ligands, twelve FDA approved antimalarial drugs were also docked with PvNMT for comparison purposes. Apart from proguanil, the other eleven antimalarial drugs displayed fewer hydrogen bonds under 3 angstroms over the 9 binding modes compared to all six of the potential hit compounds. This study discovered six compounds which displayed stronger interactions with the target protein compared to majority of the FDA approved drugs. The results of this investigation gave us new molecules that could be further investigated for the designing of novel drug-like compounds for the treatment of Malaria.
文摘Lipinski’s “Rule of Five” was introduced for predicting oral bioavailability to describe drug-like molecules. For the purpose of this research the rules were used to separate potential inhibitors of HIV-1 integrase (1BIS.pdb) into two groups: drug-like and nondrug-like. If one of Lipinski’s “Rule of Five” was not followed the potential inhibitor was classified as nondrug-like. Thirty molecules were identified from the literature, twenty-four drug-like and six nondrug-like, that were docked into the active site of 1BIS.pdb (considered the non-mutated protein) and two mutant models, Y143R and N155H. These are two of the mutations that have led to increased resistance to HIV-1 integrase drugs such as raltegravir and elvitegravir. The computational software, ICM-Pro (Molsoft L.L.C.), was used to determine the estimated binding energy (EBE) of the drug/protein complex. It was found that the nondrug-like molecules generally had a more negative EBE, that is, tighter binding with 1BIS. pdb, though there were several exceptions in the drug-like group. With the protein mutant model Y143R, the majority of drug-like (58%) and nondrug-like molecules (67%) had tighter binding. However, for the mutant model N155H, there was the same percent (46%) of drug-like molecules with tighter binding with the mutant model as with 1BIS.pdb. The drug-like molecules were used when there was a ≥1 kcal/mole difference between 1BIS.pdb and either of the two mutant models to suggest a pharmacophore with structural characteristics for an HIV-1 integrase inhibitor.
文摘An approach of using molinspiration calculations and molecular docking on PBPs （penicillin-binding proteins） and certain β-lactamases is employed to predict the molecular properties, bioactivity and resistance of newer and reference cephalosporins. The previously synthesized cephalosporins 1-8 and reference cephalosporins were subjected to extensive evaluations by calculating the molecular properties, drug-likeness scores on the bases of Lipinski＇s rule and bioactivity prediction using the method of molinspiration web-based software. The TPSA （topological polar surface area）, OH-NH interactions, n-violation and the molinspiration Log partition coefficient （miLogP） values were also calculated. The investigated cephalosporins were subjected to molecular docking study on PBPs （lpyy） and on β-lactamases produced by S. aureus, K. pneumonia, E. coil and P. auroginosa using 1-click-docking website. Molecular properties of 1-8 recorded higher ＂FPSA than cephalexin and were lower than the reference cephalosporins and do not fulfill the requirements for Lipinski＇s rule. Bioactivities of 1-8 were predicted to be less and their docking scores on PBPs were comparable to those of the reference cephalosporins, particularly ceftobiprole. The references recorded various docking scores on the above β-lactamases and as expected, cefiobiprole recorded the lowest scores on all β-lactarnases. Cephalosporins 1-8 recorded various docking scores on β-lactamases. Molecular docking studies on PBPs and β-lactamases are considered as very useful, reliable and practical approach for predicting the bioactivity scores and to afford some information about the stability and selectivity of the newly proposed cephalosporins against β-lactamases of certain pathogenic microbes, such as P. auroginosa and MRSA, by recording the relative docking scores in comparison with those of reference cephalosporins.
文摘目的优选抗HIV中药复方,通过复方小分子数据库的构建和类药性分析,为复方抗HIV活性分子研究奠定数据库基础。方法查阅文献和国内专利搜集抗HIV中药复方,优选复方确定研究对象,在中药系统药理学数据库和分析平台(traditional chinese medicine systems pharmacology database and analysis platform,TCMSP)分别下载该复方单味中药化学成分,构建复方小分子数据库,并基于"Lipinski规则"进行类药性分析。结果检索得到48个抗HIV复方,其中单味中药组成明确的复方有11个,优选双黄连粉针剂为研究对象,构建双黄连粉针剂复方小分子数据库,命名为SHLMD,包括481个化合物,包含萜类(121个)、黄酮类(61个)、苯丙素类(31个)和有机酸及其酯类(23个)等11类化合物,以萜类和黄酮类化合物居多。基于"Lipinski规则"筛选得到323个化合物,组成的新数据库命名为Lipinski-SHLMD。结论双黄连粉针剂是适合优先展开研究的抗HIV中药复方,构建的SHLMD为双黄连粉针剂的分子研究奠定了数据库基础,利用"Lipinski规则"初筛突出了研究重点。
