Analysis of secondary structure within sgm and kgmB mRNA

Sgm metiltransferaza iz soja Micromonospora zionensis i KgmB metiltransferaza iz soja Streptoalloteichus tenebrarius ostvaruju rezistenciju na aminoglikozidne antibiotike metilacijom nukleotida na poziciji G1405 u okviru A mesta na 16S rRNK. Smatra se da je za autoregulaciju sgm gena odgovoran (C)CCGCCC motiv. Najverovatnije je ista sekvenca odgovorna i za autoregulaciju kgmB gena. Po kompjuterskoj predikciji, ovaj motiv, lociran u 5' netranslatirajućem regionu iRNK molekula oba gena, bi mogao učestvovati u formiranju sekundarne strukture tipa ukosnice. Kako Sgm i KgmB metiltransferaze jedna drugu autoregulišu, moguće je da prepoznaju iste cis elemente u iRNK molekulima. Eksperimenti ispitivanja strukture su, s jedne strane potvrdili prisustvo stabilne sekundarne strukture u okviru 5' netranslatirajućeg regiona iRNK molekula sgm gena, a sa druge, nisu dokazali postojanje modelovane sekundarne strukture u iRNK molekulu kgmB gena.Sgm methyltransferase from Micromonospora zionensis and KgmB methyltransferase from Streptoalloteichus tenebrarius are resistant to aminoglycoside antibiotics as a result of their ability to specifically methylate G1405 within the bacterial 16S rRNA A-site. The (C)CGCCC motif, assumed to be a regulatory sequence responsible for the autoregulation of the sgm gene, could most likely also be responsible for the autoregulation of the kgmB gene. This sequence, found within the 5' untranslated region of both sgm and kgmB mRNAs, as indicated by in silico prediction, may be involved in the formation of a specific stem-loop structure. Sgm and KgmB are mutually down-regulated and it is likely that they share the same cis-acting elements. Structure probing experiments confirmed the existence of a stable secondary structure within the 5' UTR of the sgm mRNA, while the analysis of kgmB mRNA failed to confirm the predicted structure

Analysis of secondary structure within sgm and kgmB mRNA

Sgm methyltransferase from Micromonospora zionensis and KgmB methyltransferase from Streptoalloteichus tenebrarius are resistant to aminoglycoside antibiotics as a result of their ability to specifically methylate G1405 within the bacterial 16S rRNA A-site. The (C)CGCCC motif, assumed to be a regulatory sequence responsible for the autoregulation of the sgm gene, could most likely also be responsible for the autoregulation of the kgmB gene. This sequence, found within the 5' untranslated region of both sgm and kgmB mRNAs, as indicated by in silico prediction, may be involved in the formation of a specific stem-loop structure. Sgm and KgmB are mutually down-regulated and it is likely that they share the same cis-acting elements. Structure probing experiments confirmed the existence of a stable secondary structure within the 5' UTR of the sgm mRNA, while the analysis of kgmB mRNA failed to confirm the predicted structure.

Bioleaching of copper from samples of old flotation tailings (Copper Mine Bor, Serbia)

Bioleaching of samples taken from depths of 10, 15, and 20 m from old flotation tailings of the Copper Mine Bor was conducted in shaken flasks using the extremely acidic water of Lake Robule as lixiviant. The yields of copper after five weeks of the bioleaching experiments were 68.34 +/- 1.21 % for the 15-m sample, 72.57 +/- 0.57 % for the 20-m sample and 97.78 +/- 5.50 % for the 10-m sample. The obtained results were compared to the results of acid leaching of the same samples and it was concluded that bioleaching was generally more efficient for the treatment of samples taken from depths of 10 and 20 m. The content of pyrite in the 20-in sample, which contained the highest amount of this mineral, was reduced after bioleaching. The benefits of this approach are recovery of substantial amounts of copper, reducing the environmental impact of flotation tailings and the application of abundant and free water from the acidic Robule Lake as lixiviant. The obtained results showed that bioleaching could be more efficient than acid leaching for copper extraction from flotation tailings with higher sulfide contents

rRNA methyltransferases and their role in resistance to antibiotics

Metiltransferaze (MTaze), koje čine veliku proteinsku superfamiliju, kao donatora metil grupe najčešće koriste S-adenozil-L-metionin (SAM). SAM-zavisne MTaze metiluju nukleinske kiseline (DNK, RNK) i proteine, modulišući tako njihovu aktivnost, funkciju i strukturnu organizaciju. Metilacija G1405 ili A1408 baza u 16S rRNK mikroorganizama koji proizvode aminoglikozide obezbeđuje rezistenciju na sopstvene toksične proizvode. Ovaj mehanizam rezistencije je donedavno bio opisan samo kod proizvođača antibiotika. Od 2003. godine i kod patogenih bakterija beleži se neprestan porast rezistencije na aminoglikozide putem ovog mehanizma, što predstavlja veliku pretnju efikasnoj upotrebi aminoglikozida u kliničkoj praksi. Jedno od mogućih rešenja problema leži u razvoju novih jedinjenja koja bi efikasno delovala na nova mesta u okviru ribozoma. Drugi pristup rešavanju ovog problema uključuje razvoj inhibitora MTaza odgovornih za rezistenciju, sa idejom da se onemogući modifikacija bakterijske rRNK i na taj način vrati terapeutska efikasnost postojećim aminoglikozidima. Fundamentalna istraživanja vezana za proteinsku ekspresiju, potpuno razumevanje mehanizma rezistencije kao i razrešenje tercijarne strukture proteina su neophodan preduslov za primenu inhibitora 16S rRNK MTaza u medicini.Methyltransferases (MTases), a large protein superfamily, commonly use S-adenosyl-L-methionine (SAM) as the methyl group donor. SAM-dependant MTases methylate both nucleic acids (DNA, RNA) and proteins, and thus modulate their activity, function and folding. Methylation of G1405 or A1408 nucleotides of 16S rRNA in aminoglycoside-producing microorganisms confers the resistance to their own toxic product(s). This mechanism of resistance has been considered as unique to antibiotics producers until recently. Since 2003, methylation of 16S rRNA as a mechanism of resistance is increasingly emerging in pathogenic bacteria. This represents a major threat towards the usefulness of aminoglycosides in the clinical practice. A potential solution to the problem involves the design of novel compounds that would act against new ribosomal targets. The second approach to the issue includes the development of resistance MTases' inhibitors, with the idea to prevent them from modifying the bacterial rRNA, and thus reinstate the therapeutic power of existing aminoglycosides. As the latter approach has considerable potential, it is obvious that fundamental research related to protein expression, in-depth understanding of the mechanism of action and resolving a tertiary structure of 16S rRNAs MTases are prerequisites for application in medicine

Supplementary data for article: Aleksić, I.; Šegan, S.; Andrić, F.; Zlatović, M.; Moric, I.; Opsenica, D. M.; Senerovic, L. Long-Chain 4-Aminoquinolines as Quorum Sensing Inhibitors in Serratia Marcescens and Pseudomonas Aeruginosa. ACS Chemical Biology 2017, 12 (5), 1425–1434. https://doi.org/10.1021/acschembio.6b01149

Supporting information for: [https://doi.org/10.1021/acschembio.6b01149]Related to published version: [http://cherry.chem.bg.ac.rs/handle/123456789/2461]Related to accepted version: [http://cherry.chem.bg.ac.rs/handle/123456789/3089

Supplementary data for article: Aleksić, I.; Šegan, S.; Andrić, F.; Zlatović, M.; Moric, I.; Opsenica, D. M.; Senerovic, L. Long-Chain 4-Aminoquinolines as Quorum Sensing Inhibitors in Serratia Marcescens and Pseudomonas Aeruginosa. ACS Chemical Biology 2017, 12 (5), 1425–1434. https://doi.org/10.1021/acschembio.6b01149

Supporting information for: [https://doi.org/10.1021/acschembio.6b01149]Related to published version: [http://cherry.chem.bg.ac.rs/handle/123456789/2461]Related to accepted version: [http://cherry.chem.bg.ac.rs/handle/123456789/3089

Use of bendamustin instead of carmustin in autologous stem cell transplantation conditioning – toxicity and infectious complications comparison

Unatrag nekoliko godina u hematologiji i onkologiji globalno sve češći problem postaje prikladna opskrba „starijim i manje zanimljivim“ kemoterapeuticima. Zbog povremene nestašice karmustina, jednog od osnovnih kemoterapeutika pri kondicioniranju prije autologne transplantacije krvotvornih matičnih stanica (ATK S) u oboljelih od limfoma, u našem se centru od 2016. godine on zamjenjuje bendamustinom. U ovom radu retrospektivno analiziramo tijek ATK S-a u 41 bolesnika koji su primili bendamustin u sklopu protokola BeEA M te ga uspoređujemo s tijekom ATK S-a u 40 bolesnika koji su primili karmustin u sklopu protokola BEA M. Medijan oporavka vrijednosti neutrofila (> 0,5 × 109/l) u skupini koja je primila bendamustin iznosio je 11 dana, dok je u skupini kondicioniranoj karmustinom iznosio 10 dana. Medijan oporavka vrijednosti trombocita (> 20 × 109/l) bio je duži kod skupine koja je primala bendamustin (16 prema 13 dana) te su ti bolesnici bili duže ovisni o transfuzijama eritrocita (7 prema 5 dana). Infektivne komplikacije nisu bile češće nakon primjene bendamustina, ali smo nakon primjene karmustina imali veću pojavu mukozitisa II. – III. stupnja (35% prema 12%). Nakon primjene bendamustina zabilježen je jedan slučaj nefrotoksičnosti i kardiotoksičnosti terapije, dok kod primjene karmustina te komplikacije nisu zabilježene. Pri upotrebi bendamustina kod kondicioniranja u naših bolesnika u ovom trenutku nije utvrđena znatnija hematološka toksičnost u odnosu prema karmustinu, ali su prisutni dulji period oporavka vrijednosti trombocita te niža incidencija mukozitisa.Inadequate supply of „old and less interesting“ chemotherapeutic agents is becoming a global issue in hemato-oncology today. In 2016 we were faced with occasional carmustin shortage, one of the most commonly used in autologous transplant conditioning regimens for lymphoma in our centre, so we decided to use bendamustin instead. We performed a retrospective analysis of 41 patients treated at our centre who had received bendamustin within BeEA M protocol and compared them with 40 patients who had received carmustin within BEA M protocol. Both protocols were used as conditioning protocols before autologous stem cell transplantation. Neutrophil recovery median following transplantation (AN C>0,5x109/l) was 11 days in the bendamustin group in comparison to 10 days in the carmustin group.Platelets recovery median following transplantation (PLT>20x109/l) was longer in the bendamustin group (16 vs.13 days) as was blood transfusion dependency (7 vs. 5 days). Infectious complications were not more frequent after bendamustin, but grade II–III mucositis was more frequent in patients who received carmustin (35% vs.12%). Following bendamustin we had one reported case of nephrotoxicity and cardiac toxicity, not reported with carmustin. Bendamustin has shown similar hematologic toxicity compared to carmustin but a longer platelet recovery period and a lower mucositis incidence

Effect of structural features of antitumor histone deacetylase inhibitors

U okviru ovog diplomskog rada istražen je odnos fizičko-kemijskih svojstva i parametara toksičnosti odabranih antitumorskih inhibitora (n=31) histon deacetilaza (HDACi) koji sadrže hidroksamsku skupinu, te su provedene QSAR korelacijske studije korištenjem molekulskih deskriptora i ADMET svojstava u svrhu procjene potencijalne toksičnosti i sigurne terapijske primjene ovih inhibitora. Rezultati istraživanja su pokazali da se molekulski deskriptori i ADMET svojstva mogu uspješno primijeniti u predviđanju potencijalnih toksičnih učinaka ispitivanih HDAC inhibitora.In the frame of this diploma work, the relationship between physico-chemical properties and toxicity parameters of selected anti-tumor HDAC inhibitors (n = 31) that contain a hydroxamic acid moiety were investigated and the QSAR correlation studies were performed using molecular descriptors and ADMET properties to evaluate the potential toxicity and safety profile of the therapeutic application of these inhibitors. The results of these studies revealed that the use of molecular descriptors and ADMET parameters can be successfully applied in prediction of the potential toxic effects of investigated HDACIs

DOI:10.2298/ABS1003515V ANALYSIS OF SECONDARY STRUCTURE WITHIN SGM AND KGMB MRNA

Abstract- Sgm methyltransferase from Micromonospora zionensis and KgmB methyltransferase from Streptoalloteichus tenebrarius are resistant to aminoglycoside antibiotics as a result of their ability to specifically methylate G1405 within the bacterial 16S rRNA A-site. The (C)CGCCC motif, assumed to be a regulatory sequence responsible for the autoregulation of the sgm gene, could most likely also be responsible for the autoregulation of the kgmB gene. This sequence, found within the 5 ’ untranslated region of both sgm and kgmB mRNAs, as indicated by in silico prediction, may be involved in the formation of a specific stem-loop structure. Sgm and KgmB are mutually down-regulated and it is likely that they share the same cis-acting elements. Structure probing experiments confirmed the existence of a stable secondary structure within the 5 ’ UTR of the sgm mRNA, while the analysis of kgmB mRNA failed to confirm the predicted structure

Bioleaching of copper from old flotation tailings samples (Copper Mine Bor, Serbia)

Bioleaching of samples taken from depths of 10, 15, and 20 meters from old flotation tailings of the Copper Mine Bor was conducted in shaken flasks using extremely acidic water of Lake Robuleas lixiviant. Yield of copper after five weeks of the bioleaching experiment was 68.34±1.21% for 15 m sample, 72.57±0.57% for 20 m sample and 97.78±5.50% for 10 m sample. The obtained results were compared to the results of acid leaching of the same samples and it was concluded that bioleaching was generally more efficient for the treatment of samples taken from depths of 10 m and 20 m. The content of pyrite in the 20 m sample, which contained the highest amount of this mineral, was reduced after bioleaching. Benefits of this approach are: recovery of substantial amounts of copper, reducing the environmental impact of flotation tailings and the application of abundant and free water from the Robule acidic lake as lixiviant. Results of the experiment showed that bioleaching can be more efficient than acid leaching for copper extraction from flotation tailings with higher sulfide contents. [Projekat Ministarstva nauke Republike Srbije, br. 176016 i br. 173048