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Tytuł:
Computational study of binding of epothilone A to β-tubulin
Autorzy:
Kamel, Karol
Kolinski, Andrzej
Powiązania:
https://bibliotekanauki.pl/articles/1039930.pdf
Data publikacji:
2011
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
epothilones
β-tubulin
flexible docking
drug design
Opis:
Understanding the interactions of epothilones with β-tubulin is crucial for computer aided rational design of macrocyclic drugs based on epothilones and epothilone derivatives. Despite numerous structure-activity relationship investigations we still lack substantial knowledge about the binding mode of epothilones and their derivatives to β-tubulin. In this work, we reevaluated the electron crystallography structure of epothilone A/β-tubulin complex (PDB entry 1TVK) and proposed an alternative binding mode of epothilone A to β-tubulin that explains more experimental facts.
Źródło:
Acta Biochimica Polonica; 2011, 58, 2; 255-260
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
N-Methyl-N-D-fructosyl amphotericin B methyl ester (MF-AME), a novel antifungal agent of low toxicity: Monomer/micelle control over selective toxicity.
Autorzy:
Cybulska, Barbara
Gadomska, Ina
Mazerski, Jan
Grzybowska, Jolanta
Borowski, Edward
Cheron, Monique
Bolard, Jacques
Powiązania:
https://bibliotekanauki.pl/articles/1044402.pdf
Data publikacji:
2000
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
reactional drug design
selective toxicity
amphotericin B
Opis:
Rational chemical modification of amphotericin B (AMB) led to the synthesis of sterically hindered AMB derivatives. The selected optimal compound, N-methyl- N-D-fructosyl amphotericin B methyl ester (MF-AME) retains the broad spectrum of antifungal activity of the parent antibiotic, and exhibits a two orders of magnitude lower toxicity in vivo and in vitro against mammalian cells. Comparative studies of MF-AME and AMB comprising the determination of the spectroscopic properties of monomeric and self-associated forms of the antibiotics, the investigation of the influence of self-association on toxicity to human red blood cells, and of the antibiotic-sterol interaction were performed. On the basis of the results obtained it can be assumed that the improvement of the selective toxicity of MF-AME could in part be a consequence of the diminished concentration of water soluble oligomers in aqueous medium, and the better ability to differentiate between cholesterol and ergosterol.
Źródło:
Acta Biochimica Polonica; 2000, 47, 1; 121-131
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Novel potential anticancer agents
Autorzy:
Jęśkowiak, Izabela
Ryng, Stanisław
Powiązania:
https://bibliotekanauki.pl/articles/1178224.pdf
Data publikacji:
2018
Wydawca:
Przedsiębiorstwo Wydawnictw Naukowych Darwin / Scientific Publishing House DARWIN
Tematy:
anticancer agents
carcinoma cell lines
drug design
Opis:
Cancer is a widespread and lethal disease. It is considered as the first leading cause of deaths in economically developed countries. Nonetheless, the search for an effective treatment of cancer is still a major challenge. In this review, we analyzed the core structure of compounds and their impact on antitumor activity. Diversity of heterocyclic ring in the innovatory anticancer substances showed the potential in the design and development of new anticancer drugs.
Źródło:
World Scientific News; 2018, 93; 40-49
2392-2192
Pojawia się w:
World Scientific News
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Scoring ligand efficiency
Autorzy:
Polanski, Jaroslaw
Duszkiewicz, Roksana
Pedrys, Anna
Gasteiger, Johann
Powiązania:
https://bibliotekanauki.pl/articles/895599.pdf
Data publikacji:
2019-08-30
Wydawca:
Polskie Towarzystwo Farmaceutyczne
Tematy:
drugs
activity
drug design
ligand efficiency
PubChem
ChEMBL
Opis:
Ligand efficiency (LE) is a molecular descriptor that probes the ratio of potency vs. heavy atom count (HAC). As an estimator of drug candidates, LE emphasizes a low heavy atom count more than potency. The objective was to design a novel transform where potency and the HAC would be balanced more evenly. A series of novel descriptors SCORE was defined to evaluate the co-influence of potency and the HAC. In particular, the product ligand efficiency (PLE) was designed and tested using the data of the ChEMBL, PubChem as well as the selected series of drugs and drug-fragments.
Źródło:
Acta Poloniae Pharmaceutica - Drug Research; 2019, 76, 4; 761-768
0001-6837
2353-5288
Pojawia się w:
Acta Poloniae Pharmaceutica - Drug Research
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Selected applications of fluorinated MR contrast agents and fluorine-containing drugs in medicine
Autorzy:
Bartusik-Aebisher, Dorota
Bober, Zuzanna
Aebisher, David
Powiązania:
https://bibliotekanauki.pl/articles/895525.pdf
Data publikacji:
2020-06-29
Wydawca:
Polskie Towarzystwo Farmaceutyczne
Tematy:
drug delivery
drug design
19F MRI
19F MRS
drug efficacy
Opis:
This review aims to present magnetic resonance imaging (MRI) and magnetic resonance spectroscopy (MRS) for applications in cellular therapeutics including descriptions of the use of 19F MRI and 19F MRS in drug tracking and visualization. Both MRI and MRS are often used as diagnostic tools in oncology, are non-invasive, and also can be employed for monitoring non-oncological and oncological therapies. Herin, we provide information pertaining to tracking and visualization of fluorinated drug uptake in cancer tissue in vitro, in vivo and ex vivo. The response of tissue to treatment is also discussed.
Źródło:
Acta Poloniae Pharmaceutica - Drug Research; 2020, 77, 3; 403-410
0001-6837
2353-5288
Pojawia się w:
Acta Poloniae Pharmaceutica - Drug Research
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Modelowanie molekularne jako etap poszukiwania nowych substancji o potencjalnym znaczeniu terapeutycznym
Molecular modeling as a stage of searching for new substances with potential therapeutic significance
Autorzy:
Pisula, Magdalena
Dróżdż, Ewelina
Chełmecka, Elżbieta
Powiązania:
https://bibliotekanauki.pl/articles/1035526.pdf
Data publikacji:
2020
Wydawca:
Śląski Uniwersytet Medyczny w Katowicach
Tematy:
projektowanie leków
modelowanie molekularne
in silico
drug design
molecular modeling
Opis:
The paper is a review of the literature on molecular modeling, with particular emphasis on the use of modern in silico methods in the early stages of designing new medical substances. Its purpose is to discuss the significance and justification of using computer software in the process of creating new drugs. Therefore, the stages through which a compound must pass so that it can be considered as a good drug candidate were presented, and the subsequent stages in the proces of searching for substances using molecular modeling methods were discussed. It has been demonstrated that molecular modeling can be a useful tool in the process of designing medicinal substances, as well as an important factor reducing the costs and shortening the time spent researching a new drug. Due to the considerable effectiveness of computer methods, work should be carried out in their further development.
Praca stanowi przegląd literatury dotyczącej modelowania molekularnego, ze szczególnym uwzględnieniem użycia nowoczesnych metod in silico we wczesnych etapach projektowania nowych substancji leczniczych. Jej celem jest omówienie znaczenia oraz uzasadnienie słuszności zastosowania oprogramowania komputerowego w procesie tworzenia nowych leków. Przedstawiono etapy, przez które przechodzi związek, aby mógł być uznany za dobrego kandydata na lek, oraz omówiono kolejne fazy postępowania podczas poszukiwania substancji metodami modelowania molekularnego. Wykazano, że modelowanie molekularne może być narzędziem przydatnym w procesie projektowania substancji leczniczych; jest to również istotny czynnik redukujący koszty oraz skracający czas poświęcony na badania nad nowym lekiem. W związku ze znaczną efektywnością metod komputerowych powinno się prowadzić prace w zakresie ich dalszego rozwoju.
Źródło:
Annales Academiae Medicae Silesiensis; 2020, 74; 91-98
1734-025X
Pojawia się w:
Annales Academiae Medicae Silesiensis
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Glucosamine-6-phosphate synthase, a novel target for antifungal agents. Molecular modelling studies in drug design.
Autorzy:
Wojciechowski, Marek
Milewski, Sławomir
Mazerski, Jan
Borowski, Edward
Powiązania:
https://bibliotekanauki.pl/articles/1041368.pdf
Data publikacji:
2005
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
drug design
glucosamine-6-phosphate synthase
fungal infections
glutamine amidotransferases
molecular modelling
Opis:
Fungal infections are a growing problem in contemporary medicine, yet only a few antifungal agents are used in clinical practice. In our laboratory we proposed the enzyme L-glutamine : D-fructose-6-phosphate amidotransferase (EC 2.6.1.16) as a new target for antifungals. The structure of this enzyme consists of two domains, N-terminal and C-terminal ones, catalysing glutamine hydrolysis and sugar-phosphate isomerisation, respectively. In our laboratory a series of potent selective inhibitors of GlcN-6-P synthase have been designed and synthesised. One group of these compounds, including the most studied N3-(4-methoxyfumaroyl)-l-2,3-diaminopropanoic acid (FMDP), behave like glutamine analogs acting as active-site-directed inactivators, blocking the N-terminal, glutamine-binding domain of the enzyme. The second group of GlcN-6-P synthase inhibitors mimic the transition state of the reaction taking place in the C-terminal sugar isomerising domain. Surprisingly, in spite of the fact that glutamine is the source of nitrogen for a number of enzymes it turned out that the glutamine analogue FMDP and its derivatives are selective against GlcN-6-P synthase and they do not block other enzymes, even belonging to the same family of glutamine amidotransferases. Our molecular modelling studies of this phenomenon revealed that even within the family of related enzymes substantial differences may exist in the geometry of the active site. In the case of the glutamine amidotransferase family the glutamine binding site of GlcN-6-P synthase fits a different region of the glutamine conformational space than other amidotransferases. Detailed analysis of the interaction pattern for the best known, so far, inhibitor of the sugar isomerising domain, namely 2-amino-2-deoxy-d-glucitol-6-phosphate (ADGP), allowed us to suggest changes in the structure of the inhibitor that should improve the interaction pattern. The novel ligand was designed and synthesised. Biological experiments confirmed our predictions. The new compound named ADMP is a much better inhibitor of glucosamine-6-phosphate synthase than ADGP.
Źródło:
Acta Biochimica Polonica; 2005, 52, 3; 647-653
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Assessment of the free binding energy of 1,25-dihydroxyvitamin D3 and its analogs with the human VDR receptor model
Autorzy:
Kamel, Karol
Kolinski, Andrzej
Powiązania:
https://bibliotekanauki.pl/articles/1039678.pdf
Data publikacji:
2012
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
KH 1060
drug design
docking
EB 1089
vitamin D
RO 25-9022
Opis:
1,25-dihydroxyvitamin D3 has quite significant anticancer properties, but its strong calcemic effect in principle excludes it as a potential anticancer drug. Currently, a lot of effort is being devoted to develop potent anticancer analogs of 1,25-dihydroxyvitamin D3 that would not induce hypercalcemia during therapy. In this work, the free binding energy of the VDR receptor with 1,25-dihydroxyvitamin D3 and its three potent analogs (EB 1089, KH 1060 and RO 25-9022) is calculated and compared with each other. With this approach, we could estimate the relative binding affinity of the most potent analog, RO 25-9022, and also revealed a quite distinct mechanism of its interaction with VDR.
Źródło:
Acta Biochimica Polonica; 2012, 59, 4; 653-660
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Virtual screening strategies in drug design – methods and applications
Autorzy:
Bielska, E.
Lucas, X.
Czerwoniec, A.
Kasprzak, J.M.
Kaminska, K.H.
Bujnicki, J.M.
Powiązania:
https://bibliotekanauki.pl/articles/80139.pdf
Data publikacji:
2011
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
virtual screening
drug design method
application
drug discovery
similarity search
drug development
high-throughput screening
medical chemistry
chemical compound
experimental approach
Źródło:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2011, 92, 3
0860-7796
Pojawia się w:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Possible computational filter to detect proteins associated to influenza A subtype H1N1
Autorzy:
Polanco, Carlos
Buhse, Thomas
Castañón-González, Jorge
Samaniego, José
Powiązania:
https://bibliotekanauki.pl/articles/1039197.pdf
Data publikacji:
2014
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
Polarity Index Method
influenza A virus subtype H1N1
drug design
QSAR method
Opis:
The design of drugs with bioinformatics methods to identify proteins and peptides with a specific toxic action is increasingly recurrent. Here, we identify toxic proteins towards the influenza A virus subtype H1N1 located at the UniProt database. Our quantitative structure-activity relationship (QSAR) approach is based on the analysis of the linear peptide sequence with the so-called Polarity Index Method that shows an efficiency of 90% for proteins from the Uniprot Database. This method was exhaustively verified with the APD2, CPPsite, Uniprot, and AmyPDB databases as well as with the set of antibacterial peptides studied by del Rio et al. and Oldfield et al.
Źródło:
Acta Biochimica Polonica; 2014, 61, 4; 693-698
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Electrostatics in computer-aided drug design
Autorzy:
Naray-Szabo, G.
Matyus, P.
Powiązania:
https://bibliotekanauki.pl/articles/1953955.pdf
Data publikacji:
1998
Wydawca:
Politechnika Gdańska
Tematy:
electrostatics
drug design
molecular electrostatic potential
molecular electrostatic field
similarity
pharmacophore
ComFa method
protein-ligand interaction
Opis:
Hydrogen bonds and charge-charge interactions, determined by molecular electrostatics, play essential role in biopolymer-ligand associations. Accordingly, electrostatics is crucial in the qualitative and quantitative characterisation of the binding of drugs to their target molecules. In the following, we will give an account on the role of molecular electrostatics in a drug design, laying emphasis on our own work. We will survey the most important computation methods of molecular electrostatic potentials, then outline basic aspects of molecular recognition: steric, electrostatic and hydrophobic complementarity. On the basis of the complementarity, we will also define molecular similarity and discuss various applications of these concepts to the treatment of protein-ligand interactions and a rational drug design. Special attention will be paid to a receptor mapping and to a comparative molecular field analysis, with some our recent applications. A further important point will be the molecular electrostatic field (potential gradient) as a hydrophobicity measure. We will argue that the hydrophobic complementarity and similarity can be treated on the basis of matching regions of the interacting molecules that are characterised by a similar magnitude of the electrostatic field. The concept of the electrostatic complementarity will be extended to enzyme-substrate interactions, providing a firm basis for the quantitative estimation of catalytic rate enhancement.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 1998, 2, 4; 551-562
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Natural products as potential inhibitors of FLT3 for acute myeloid leukemia: HTVS, docking, and molecular dynamic simulation
Autorzy:
Salah, Salsabeel
Sami, Najat
Ali, Sarah
Khalid, Teemah-Alrahman
Alnajjar, Radwan
Powiązania:
https://bibliotekanauki.pl/articles/35500319.pdf
Data publikacji:
2023
Wydawca:
Radomskie Towarzystwo Naukowe
Tematy:
acute myeloid leukemia
drug design
anticancer
CADD
FLT3
ostra białaczka szpikowa
projektowanie leków
terapia antynowotworowa
Opis:
Cancer is one the most common health issues worldwide, with cancer-related mortality of 9.5 million in 2018, with an expectation to become 29.5 by 2040. Among others, acute myeloid leukemia (AML) is common among older people. FLT3 mutations are one of the most common genetic aberrations found in Acute Myeloid Leukemia and are associated with poor prognosis. Herein, we attempt to identify natural compounds as potential candidates to treat AML by targeting the FLT3 kinase domain using in silico approaches. The COCONUT database, which contains 407,270 natural compounds, was HTVS against the FLT3 kinase domain active site, and promising compounds were subject to molecular docking. Finally, frontier compounds were validated further using molecular dynamic simulation. In total, ten compounds were identified with docking scores higher than Quizartinib (-11.606 kcal/mol), with the best three compounds showing a docking score of -18.052, -15.772, and -16.767 kcal, respectively, and compound 2 showing excellent stability in molecular dynamic simulation.
Źródło:
Scientiae Radices; 2023, 2, 4; 325-346
2956-4808
Pojawia się w:
Scientiae Radices
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Witaminy z grupy B : opis właściwości fizykochemicznych oraz bioaktywności z wykorzystaniem przykładowych narzędzi cheminformatycznych
B vitamins : description of physicochemical properties and bioactivity by exemplary cheminformatics tools
Autorzy:
Banach, Sylwia
Jezierska, Aneta
Powiązania:
https://bibliotekanauki.pl/articles/27310030.pdf
Data publikacji:
2023
Wydawca:
Polskie Towarzystwo Chemiczne
Tematy:
witaminy B
cheminformatyka
chemia medyczna
projektowanie leków
molinspiration
bioaktywność
B vitamins
cheminformatics
medicinal chemistry
drug design
bioactivity
Opis:
This paper presents a literature review of the biochemistry of vitamins B and the results of in silico physicochemical properties and bioactivity studies. The description was performed by cheminformatics tools closely related to the field of Medicinal Chemistry. It allows us to predict a great number of properties e.g. logP, TPSA, molecular volume or bioactivity associated with the chosen proteins (like kinases, proteases etc.). These investigations were carried out with the use of cheminformatics web tool Molinspiration. Its great advantages are mainly its wide availability, ease of application and quick analysis of small compounds. Thanks to the comparison with literature data of well–known B vitamins, it is possible to confirm that current cheminformatic web tools provide high reliability of the results and can support Drug Design methods.
Źródło:
Wiadomości Chemiczne; 2023, 77, 9-10; 873--896
0043-5104
2300-0295
Pojawia się w:
Wiadomości Chemiczne
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Docking for drug interface residues of modelled VPS33B of human with PtpA of Mycobacterium tuberculosis CDC1551
Autorzy:
Reddy, K.M.
Pattathil, M.D.
Jayachandra, S.Y.
Parameshwar, A.
Sulochana, M.B.
Powiązania:
https://bibliotekanauki.pl/articles/11443.pdf
Data publikacji:
2014
Wydawca:
Przedsiębiorstwo Wydawnictw Naukowych Darwin / Scientific Publishing House DARWIN
Tematy:
antigenicity
protein-protein interaction
network
homology modelling
drug design
interface residue
Mycobacterium tuberculosis
man
protein
biological function
Opis:
VPS33B, a human Vacuolar Protein Sorting (VPS) protein which mediates the phagolysosomal fusion in macrophage of the eukaryotic organisms. This protein has a great role during the mycobacterial infections, which binds with the Mycobacterium protein tyrosine phosphatase A (PtpA). A single functional domain of PtpA has been identified using SMART domain databases, followed by finding the antigenicity of PtpA using CLC main workbench tool. The protein-protein interaction network predicts the interface of biological functions of proteins, built by using Cytoscape 2.8.3 version tool for manual literature survey of protein sets. According to the literature the specific interactivity of PtpA with VPS33B of human lead to pathogenesis, and provided a good platform to find the structure of VPS33B as it lacks the 3 dimensional structure in PDB. Homology Modelling of VPS33B provides a significant properties to design a specific drug through screening the drug databases (eDrug3D). The modelled protein has been validated through SAVES server maintained by NIH and UCLA with the standard Ramachandran plot with accuracy of 90.7 %. From our findings the interface residues are very crucial points which has been found through docking the modelled protein and Mycobacterium protein and interface residues were selected manually using PyMol software.
Źródło:
International Letters of Natural Sciences; 2014, 11, 2
2300-9675
Pojawia się w:
International Letters of Natural Sciences
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Investigation of interactions between dermorphin analogs and µ-opioid receptor
Autorzy:
Karczyńska, A.
Zaborowski, B.
Ślusarz, M.
Powiązania:
https://bibliotekanauki.pl/articles/1935820.pdf
Data publikacji:
2014
Wydawca:
Politechnika Gdańska
Tematy:
molecular modeling
opioid receptors
defmorphin
molecular docking
drug design
modelowanie molekularne
receptory opioidowe
dokująca molekularna
projektowanie leków
dermorfina
Opis:
Opioid receptors play the pain control function in the body. Most of the research is carried out to find the most effective analgesic. The earliest analgesic is morphine, however, unfortunately it has many side effects [Mizoguchi H et al. 2003 J. Pharmacol Sci. 93 423]. At a later time dermorphin was discovered as another potent analgesic [Mont ecucchi P C et al. 1981 Int. J. Pept. Protein Res. 17 275]. Unfortunately, this peptide is not resistant to enzymatic metabolism [Kisara K et al. 1986 Br. J. Pharmacol. 87 183; Sasaki Y et al. 1985 Neuropeptides 5 391]. The objective of this study is to search for new opioid analgesics by investigation of interactions between dermorphin analogs and the μ -opioid receptor using molecular modeling methods. MOPR ( μ -Opioid Peptide Receptor) complexes with several ligands (with known biological activity) were modeled to explain how the structure of the complex was related to the biological activity. The investigated dermorphin analogs containing [ DMT1, D -Arg 2 ] (especially tetrapeptides) may become a good alternative for the currently used an algesics.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2014, 18, 4; 331--336
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
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