scholarly journals In Silico ADME/T Properties of Quinine Derivatives using SwissADME and pkCSM Webservers

Author(s):  
Jean Gonfi M. Mvondo ◽  
Aristote Matondo ◽  
Dani T. Mawete ◽  
Sylvie-Mireille N. Bambi ◽  
Blaise M. Mbala ◽  
...  

Aim: Malaria is among the most devastating and widespread tropical parasitic diseases. To overcome antimalarial drug resistance, new drugs need to be developed. This study is designed to establish the pharmacokinetic profile and toxicity of nine quinine derivatives as potential antimalarial drugs using in silico approaches by SwissADME and pkCSM. Methodology: The structures of investigated compounds were translated into canonical SMILES format and then submitted to SwissADME web tool that gives free access to physicochemical properties, pharmacokinetics, drug-likeness and medicinal chemistry friendliness of compounds, and pkCSM webserver for predicting and optimizing pharmacokinetic and toxicity properties. Results: SwissADME mainly used to predict the physicochemical properties of compounds and their drug-likeness revealed that all quinine derivatives have good bioavailability and satisfied the Lipinski’s rule of five. The pkCSM results on the absorption, distribution, metabolism, excretion and toxicity show  that all investigated compounds have a good pharmacokinetic profile and they are safe since they belong to class 4 of the Globally Harmonized System (300 < Category 4 ≤ 2000 mg/kg/day). Conclusion: Drug-likeness and ADME/T predictions of nine investigated quinine derivatives revealed that they are good candidates to oral drug formulation and thus they can be used in a broader context of overcoming the development of resistance by Plasmodium protozoans against most of the drugs currently used to treat malaria. As future prospects, further studies on bioevaluation of compounds are needed to elucidate their potential pharmacological activities.

Author(s):  
Jainey Pj ◽  
Ishwar Bhat K

Objectives: Nitrogen containing heterocyclic compounds plays an important role in medicinal chemistry. Among them, five-membered ring pyrazolines have found to possess many biological and pharmacological activities like anticancer, antitubercular, antimicrobial, anti-inflammatory etc. Objective is to determine the physicochemical and drug like properties of the synthesized pyrazolines by in silico methods and to screen their antidiabetic and antioxidant activities.Methods: Chalcones were synthesized from naphthaldehydes by condensing with various substituted acetophenones in ethanol and cyclized into pyrazolines using semicarbazides/thiosemicarbazides by conventional and microwave oven synthesis. The physicochemical and drug like properties were determined by using computational tools. Antidiabetic activity was evaluated by alpha amylase inhibition assay method. Antioxidant activity studies were done by DPPH and nitric oxide method.Results: Pyrazolines were synthesized from chalcones. Microwave irradiated synthesis of chalcone was carried out to get higher yield with less reaction time period as compared to conventional method. The synthesized pyrazolines produces yield around 68% (conventional) and 85% (microwave). In silico studies showed considerable values satisfying all the parameters of physicochemical and Lipinski’s rule of five properties.  Among the compounds tested for antidiabetic and antioxidant studies, some showed promising activity.Conclusion: Physiochemical and drug like properties revealed that these compounds have good bioavailability and druglikeness properties. So these compounds are found to be interesting lead molecules for further synthesis as antidiabetic and antioxidant agents.Keywords: Chalcones, pyrazolines, in silico physicochemical properties, biological activities. 


2020 ◽  
Vol 27 (9) ◽  
pp. 1397-1406
Author(s):  
Xiaoxia Chen ◽  
Hao Li ◽  
Lichao Tian ◽  
Qinwei Li ◽  
Jinxiang Luo ◽  
...  

2019 ◽  
Vol 4 (4) ◽  
pp. 606-608 ◽  
Author(s):  
D. Giles ◽  
V.N. Saiprabha ◽  
G. Yeshna

The present work deals with the design of 7-azaindole derivatives for its Raf-B inhibition. All the designed compounds follows Lipinski’s rule of five. In silico ADME predictions of all the designed compounds suggests that none of the compounds have problem with bioavailability. The compounds were designed on the binding affinity towards the Raf-B inhibition. It was observed that few of the designed compounds were found to have significant interaction with the active site of the receptor. The compounds possessing 3-hydroxyl-2-methyl as substitution in chalcone was found to possess maximum docking score than other designed compounds.


2019 ◽  
Vol 7 (4) ◽  
Author(s):  
Hermawan Setyo Widodo ◽  
Tridjoko Wisnu Murti ◽  
Ali Agus ◽  
Widodo Widodo

Susu kambing memiliki komponen protein salah satunya protein β dan secara umum terjadi polimorfisme pada level protein. Perubahan urutan asam amino akibat polimorfisme memungkinkan adanya potensi dihasilkannya peptida bioaktif penghambat enzim pengubah angiotensin (ACEi). Penelitian ini bertujuan untuk menyaring peptida bioaktif yang berpotensi sebagai ACEi dari kasein β kambing beserta polimorfismenya. Penelitian ini dilakukan dengan teknik in silico terhadap sekuen kasein β kambing serta struktur tiga dimensi human testicular ACE. Langkah yang dilakukan dalam penelitian ini meliputi simulasi pemotongan peptida dengan enzim pencernaan (pepsin, tripsin dan kimotripsin), peninjauan karakteristik peptida lalu simulasi docking ligan-reseptor. Tampilan parameter Lipinski’s Rule of Five (Ro5), bioaktivitas dan energi afinitas dipertimbangkan untuk memilih peptida bioaktif. Hasil yang didapat menunjukkan bahwa ditemukan peptida bioaktif yakni INK (Ile-Asp-Lys) yang memiliki kemampuan hampir setara dengan lisinopril (afinitas energi -8,2kkal/mol vs. -8,3kkal/mol). Peptida INK dapat ditemukan dari hasil hidrolisis dari alel A, C, D dan E, sehingga polimorfisme tidak menyebabkan perbedaan produksi peptida bioaktif. Kesimpulan yang dapat diambil yakni kasein β susu kambing jika dicerna dengan enzim pencernaan dapat menghasilkan peptida bioaktif ACEi yakni INK.Identification of Angiotensin Converting Enzyme-inhibitor (ACEi) Bioactive Peptide from Goat Milk β-Casein with It's Polymorphism by In Silico TechniqueAbstractPolymorphism eventually may be occurred at the protein level. Changes in the amino acid sequence due to polymorphism may exhibit a potential action to generate of the angiotensin-converting enzyme inhibitors (ACEi) bioactive peptide. This study is aimed to assess bioactive peptides that have a great potent value as ACEi from goat β casein along with its polymorphism. The research was done by in silico technique on goat β-casein sequence and three-dimensional structure human testicular ACE. Peptide-cutting simulations with digestive enzymes (pepsin, trypsin and chymotrypsin), peptide properties review, then ligand-receptor docking simulations was applied in this research. Appearance of Lipinski's Rule of Five (Ro5), bioactivity and affinity energy were considered for selecting bioactive peptides. The results show that bioactive peptide found as INK (Ile-Asp-Lys) which had similar ability as lisinopril (energy affinity –8.2kcal/mol vs. –8.3kcal/mol). The INK peptides could be found from the hydrolysis resulted in alleles A, C, D and E, therefore polymorphism did not affect the differences of production of bioactive peptides. A conclusion, processed goat milk β casein with digestive enzymes could produce ACEi of INK as bioactive peptide.


Author(s):  
Kouakou Kouakou Jean-Louis ◽  
◽  
Melalie Keita ◽  
Akori Elvice Esmel ◽  
Brice Dali ◽  
...  

Background: In recent years, there has been a growing interest in Denv NS5 inhibition, with several reported RdRp inhibitors such as sulfonylbenzamides, non-nucleo-side inhibitors without any 3D-QSAR pharmacophore (PH4) available. In this context, we report here, in silico design and virtual evaluation of novel sulfonylbenzamides Denv RdRp inhibitors with favorable predicted pharmacokinetic profile. Methods: By using in situ modifications of the crystal structure of 5-(5-(3-hydroxyprop-1-yn-1-yl)thiophen-2-yl)-4- methoxy-2-methyl-N-(methylsulfonyl) benzamide (EHB)-RdRp complex (PDB entry 5HMZ), 3D models of RdRp-EHBx complexes were prepared for a training set of 18 EHBs with experimentally determined inhibitory potencies (half-maximal inhibitory concentrations IC50exp). In the search for active conformation of the EHB1-18, linear QSAR model was prepared, which correlated computed gas phase enthalpies of formation ∆∆HMM of RdRp-EHBx complexes with the IC50exp. Further, considering the solvent effect and entropy changes upon ligand binding resulted in a superior QSAR model correlating computed complexation Gibbs free energies (∆∆Gcom). The successive pharmacophore model (PH4) generated from the active conformations of EHBs served as a virtual screening tool of novel analogs included in a virtual combinatorial library (VCL) of compounds with scaffolds restricted to phenyl. The VCL filtered by the Lipinski’s rule-of-five was screened by the PH4 model to identify new EHB analogs. Results: Gas phase QSAR model: -log10(IC50exp) = p IC50exp =-0.1403 x ∆∆HMM _ 7.0879, R2 = 0.73; superior aqueous phase QSAR model: p IC50exp = -0.2036 x ∆∆Gcom + 7.4974, R2 = 0.81 and PH4 pharmacophore model: p IC50exp = 1.0001 x p IC50pre -0.0017, R2 = 0.97. The VCL of more than 30 million EHBs was filtered down to 125,915 analogs Lipinski’s rule. The five-point PH4 screening retained 329 new and potent EHBs with predicted inhibitory potencies p IC50pre up to 30 times lower than that of EHB1 (IC50exp = 23nM). Predicted pharmacokinetic profile of the new analogs showed enhanced cell membrane permeability and high human oral absorption compared to the alone drug to treat dengue virus. Conclusions: Combined use of QSAR models, which considered binding of the EHBs to RdRp, pharmacophore model and ADME properties helped to recognize bound active conformation of the sulfonylbenzamide inhibitors, permitted in silico screening of VCL of compounds sharing sulfonylbenzamide scaffold and identify new analogs with predicted high inhibitory potencies and favorable pharmacokinetic profiles. Keywords: ADME properties prediction, Dengue, 3-(5-ethynylthiophen-2-yl)-N-hydrosulfonylbenzamides, in silico screening, RNA-dependent RNA polymerase.


2021 ◽  
Vol 72 (2) ◽  
pp. 159-169
Author(s):  
OLUWAKEMI EBENEZER ◽  
MICHAEL SHAPI

Abstract Some compounds reported as active against SARS CoV were selected, and docking studies were performed using the main protease of SARS CoV-2 as the receptor. The docked complex analysis shows that the ligands selectively bind with the target residues and binding affinity of amentoflavone (–10.1 kcal mol–1), isotheaflavin-3’-gallate (–9.8 kcal mol–1), tomentin A and D (–8.0 and –8.8 kcal mol–1), theaflavin-3,3’-digallate (–8.6 kcal mol–1), papyriflavonol A (–8.4 kcal mol–1), iguesterin (–8.0 kcal mol–1) and savinin (–8.3 kcal mol–1) were ranked above the binding affinity of the reference, co-crystal ligand, ML188, a furan-2-carboxamide-based compound. To pinpoint the drug-like compound among the top-ranked compounds, the Lipinski’s rule of five and pharmacokinetic properties of all the selected compounds were evaluated. The results detailed that savinin exhibits high gastrointestinal absorption and can penetrate through the blood-brain barrier. Also, modifying these natural scaffolds with excellent binding affinity may lead to discovering of anti-SARS CoV agents with promising safety profiles.


Coronaviruses ◽  
2021 ◽  
Vol 02 ◽  
Author(s):  
Habibu Tijjani ◽  
Adamu Idris Matinja ◽  
Ahmed Olatunde ◽  
Maryam Haladu Zangoma ◽  
Abubakar Mohammed ◽  
...  

Background: The recent reemergence of the coronavirus (COVID-19) caused by the virus severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has prompted for the search of effective treatments in forms of drugs and vaccines. Aim: In this regards, we performed an in silico studies of 39 active antidiabetic compounds from medicinal plants to provide insight into their possible inhibitory potentials against SARS-CoV-2 replications and post-translational modifications. Top 12 active antidiabetic compounds with potential for dual inhibition of the replications and post-translational modifications of SARS-CoV-2 were analyzed. Results: Boswellic acids, celastrol, rutin, sanguinarine, silymarin and withanolides expressed binding energy for 3- chymotrypsin-like protease (3CLpro) (-8.0 to -8.9 Kcal/mol), papain-like protease (PLpro) (-9.1 to -10.2 Kcal/mol) and RNA-dependent RNA polymerase (RdRp) (-8.5 to -9.1 Kcal/mol) which were higher than that of the reference drugs (Lopinavir and Remdesivir) used in this study. Sanguinarine, silymarin and withanolides are most drugable phytochemicals among the other following phytochemicals as they obey the Lipinski’s rule of five analyses. Sanguinarine, silymarin and withanolides express moderately soluble with no hepatotoxicity, while silymarin and withanolides cannot permeate the blood-brain barrier and showed no Salmonella typhimurium reverse mutation assay (AMES) toxicity, unlike sanguinarine from the predictive absorption, distribution, metabolism, elimination, and toxicity (ADMET) studies. Conclusion: Sanguinarine, silymarin and withanolides could be proposed for further experimental studies for their development as possible phytotherapy for the COVID-19 pandemic.


2021 ◽  
Vol 17 (1) ◽  
pp. 83
Author(s):  
Richa Mardianingrum ◽  
Kamiel Roesman Bachtiar ◽  
Susanti Susanti ◽  
Aas Nuraisah Aas Nuraisah ◽  
Ruswanto Ruswanto

<p>Inflamasi merupakan suatu respon dari tubuh terhadap adanya cedera maupun infeksi yang ditandai dengan timbulnya kemerahan, demam, bengkak, nyeri dan hilangnya fungsi. Inflamasi berkontribusi terhadap ketidakseimbangan sekresi sitokin yang akan menghambat terjadinya apoptosis pada sel kanker sehingga menyebabkan hiperproliferasi sel. Kanker payudara merupakan salah satu penyakit kanker dengan prevalensi tertinggi di urutan ke dua di dunia. Penelitian terdahulu melaporkan pemberian minyak atsiri rimpang bangle<em> </em>(<em>Zingiber purpureum </em>Roxb.) secara topikal mampu memberikan penghambatan inflamasi yang lebih tinggi daripada <em>triamcinolone</em>, namun spesifik senyawa yang berpotensinya belum diketahui. Tujuan dari penelitian ini, yakni mencari senyawa aktif hasil analisis GCMS minyak atsiri rimpang bangle yang berpotensi sebagai antiinflamasi dan antikanker payudara secara <em>in silico</em>. Metode yang digunakan berupa <em>screening</em> <em>Lipinski’s rule of Five</em>, farmakokinetika dan toksisitas senyawa hasil analisis GC-MS, serta penambatan molekul dan dinamika molekular. Hasil<em> screening</em> dan simulasi penambatan molekul menunjukkan bahwa senyawa 1,4<em>-naphthalenedione-</em>2<em>-ethyl-3-hydroxy </em>dapat berikatan dengan reseptor COX-1 (antiinflamasi), dan hERα (antikanker payudara), namun lebih selektif terhadap reseptor COX-1 dengan nilai energi bebas (ΔG) yang lebih kecil yakni sebesar -7,20 kkal/mol, dibandingkan dengan interaksinya terhadap reseptor Erα yang bernilai -6,00 kkal/mol. Hasil simulasi dinamika molekular menggunakan metode kalkulasi MM-GBSA menunjukkan bahwa kompleks (1,4<em>-naphthalenedione-</em>2<em>-ethyl-</em>3<em>-hydroxy)</em>-(COX-1) memiliki nilai ∆G<sub>TOTAL </sub>sebesar -24,22 kkal/mol. Nilai ini lebih kecil dibandingkan dengan ∆G<sub>TOTAL </sub>kompleks (1,4-<em>naphthalenedione-</em>2<em>-ethyl-</em>3<em>-hydroxy</em>)-(hErα) sebesar -8,92 kkal/mol). Hal ini menunjukkan bahwa tingkat afinitas 1,4<em>-naphthalenedione-</em>2<em>-ethyl-</em>3<em>-hydroxy</em> terhadap COX-1 diprediksi lebih baik dan lebih poten sebagai antiinflamasi dibandingkan sebagai antikanker payudara.</p><p><strong><em>In Silico</em> Study of 1,4<em>-Naphthalenedione-</em>2<em>-Ethyl-</em>3<em>-Hydroxy</em> Compounds as Anti-inflamation dan Breast Anticancer</strong>. Inflammation is a response from the body to injury or infection which is characterized by redness, fever, swelling, pain, and loss of function. Inflammation contributes to the imbalance of cytokine secretion which will inhibit apoptosis in cancer cells, causing cell hyperproliferation. Breast cancer is one of the cancer diseases with the second-highest prevalence in the world. The pioneering works reported that topical application of Bangle (<em>Zingiber purpureum</em> R) was able to provide a higher inhibition of inflammation than triamcinolone, however, the specific potential of the compound was unknown. The purpose of this study is to find active compounds that have the potential to be anti-inflammatory and anti-cancer in the breast using <em>in silico</em> approach. The methods used are screening Lipinski’s Rule of Five,<em> </em>pharmacokinetics and toxicity of compounds from GC-MS analysis and molecular docking, and molecular dynamics. The screening and molecular docking simulation results showed that the compound 1,4-naphthalenedione-2-ethyl-3-hydroxy can bind to COX-1 (anti-inflammatory), and ERα (Estrogen Reseptor α), but was more selective towards COX-1 receptor with a binding affinity (ΔG) -7.20 kcal/mol, compare to its interaction with ERα which is -6.00 kcal/mol. The results of molecular dynamics simulation using the MM-GBSA calculation method show that the complex (1,4-naphthalenedione-2-ethyl-3-hydroxy)-(COX-1) has a value of ∆G<sub>TOTAL</sub> of -24.22 kcal/mol). This value is smaller than ∆G<sub>TOTAL</sub> of the complex (1,4-naphthalenedione-2-ethyl-3-hydroxy)-(hErα) of -8.92 kcal/mol. The results indicate that the affinity level of 1,4-naphthalenedione-2-ethyl-3-hydroxy to COX-1 was predicted to be better and more potent as an anti-inflammatory than as an anti-breast cancer.</p>


Author(s):  
Shraddha Phadke ◽  
Devender Pathak ◽  
Rakesh Somani

Aims: Design and in silico studies of 2,5-disubstituted triazole and thiadiazole derivatives as Pteridine Reductase 1 inhibitors. With a view to develop effective agents against Leishmaniasis, 2-substituted-5-[(1H-benzimidazol-2yl) methyl] azole derivatives (A1-A12) were designed against the target enzyme Pteridine reductase 1. Methodology: The series was designed by targeting Pteridine reductase 1 which is an enzyme responsible for folate and pterin metabolism. Based on thorough study of the enzyme structure and structural features of ligands required for optimum interaction with the enzyme, a series of 12 compounds consisting of 2,5-disubstituted 1,2,4-triazole and 1,3,4-thiadiazole derivatives was designed. In silico studies were carried out which included docking studies (using V Life software) to understand binding of the compounds with enzyme PTR1, ADMET studies, drug likeness studies for physicochemical properties and bioactivity studies to understand the possible mechanism of action of the compounds. These studies were undertaken using online softwares, molinspiration and admetSAR web servers. Results: Compounds A10 and A12 gave the best docking scores of -59.9765 and -60.4373 respectively that were close to dihydrobiopterin (original substrate). All the compounds complied with Lipinski’s rule of five. Most of the compounds displayed favorable ADMET properties. Conclusion: The 2,5-disubstituted 1,2,4-triazole and 1,3,4-thiadiazole derivatives exhibited good binding affinity for PTR1 enzyme (PDB code: 1E92). The docking scores indicated that enzyme binding may be governed by the nature and size of the substituents on the azole ring. The compounds display well-defined drug-like and pharmacokinetic properties based on Lipinski’s rule of five with additional physicochemical and ADMET parameters. Bioactivity studies suggested the possible drug mechanism as enzyme inhibition. Hence, this study provides evidence for consideration of valuable ligands in 2,5-disubstituted 1,2,4-triazole and 1,3,4-thiadiazole derivatives as potential pteridine reductase 1 inhibitor and further in vitro and in vivo investigations may prove its therapeutic potential.


2021 ◽  
Author(s):  
Love Edet Mendie ◽  
S Hemalatha

Abstract Drug delivery in a safe manner is a major challenge in the drug development process. Growth factor receptors (GFRs) are known to have profound roles in the growth and progression of cancerous cells making these receptors a therapeutic target in the effective treatment of cancer. This work focused on exploring bioactive compounds that can target GFRs usingin-silico method. In this study, 50 bioactive compounds from different plant sources were screened as anticancer agent against GFRs using drug likeness parameters of Lipinski’s rule of five. The molecular docking was performed between phytochemicals and GFRs. Ligands with acceptable drug likeness and binding energy comparable to the standard drugs were further screened to determine their pharmacokinetic activities. This study showed phytochemicals with the binding energy comparable with the standard drugs (Dovitinb and Geftinib), while ADME, bioactivity score and bioavailability radar analysis gave further insight on these compounds as potent anticancer agents.


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