Zayan Alhalabi

Diese Dissertation konzentriert sich auf die Anwendung von Methoden des computergestützten Wirkstoffdesigns im Kontext der Entdeckung neuer Enzyminhibitoren und der Rationalisierung von Interaktionen mit deren Zielproteinen. Die untersuchten Inhibitoren sind in der Lage lebenswichtige Proteinstrukturen wie Sirtuine und Cholinesterasen zu hemmen. Um neue Inhibitoren für herausfordernde Zielstrukturen zu entdecken, wurden Methoden des computergestützten Wirkstoffdesigns angewandt. Die verwendeten rechnergestützten Methoden kombinieren Homologiemodellierung, Docking, Molekulardynamiksimulationen, virtuelles Screening und die Analyse von Protein-Ligand-Interaktionen. Die Kombinierung von Informationen aus computergestützten Studien mit synthetischer Chemie und enzymatischen Tests half bei der Entdeckung neuer Inhibitoren für mehrere der sieben Sirtuin-Isoformen.

Sirtuins are nicotinamide adenine dinucleotide (NAD⁺)-dependent class III histone deacetylases, which have been linked to the pathogenesis of numerous diseases, including HIV, metabolic disorders, neurodegeneration and cancer. Docking of the virtual pan-African natural products library (p-ANAPL), followed by in vitro testing, resulted in the identification of two inhibitors of sirtuin 1, 2 and 3 (sirt1-3). Two bichalcones, known as rhuschalcone IV () and an analogue of rhuschalcone I (), previously isolated from the medicinal plant, were shown to be active in the in vitro assay. The rhuschalcone I analogue () showed the best activity against sirt1, with an ICvalue of 40.8 µM. Based on the docking experiments, suggestions for improving the biological activities of the newly identified hit compounds have been provided.

Nonpolar derivatives of heterocyclic aromatic screening hits like the non-selective sirtuin inhibitor splitomicin tend to be poorly soluble in biological fluids. Unlike sp(3) -rich natural products, flat aromatic compounds are prone to stacking and often difficult to optimize into leads with activity in cellular systems. The aim of this work was to identify anchor points for the introduction of sp(3) -rich fragments with polar functional groups into the newly discovered active (IC50  = 5 μM) but nonpolar scaffold 1,2-dihydro-3H-naphth[1,2-e][1,3]oxazine-3-thione by a molecular modeling approach. Docking studies were conducted with structural data from crystallized human SIRT2 enzyme. Subsequent evaluation of the in silico hypotheses through synthesis and biological evaluation of the designed structures was accomplished with the aim to discover new SIRT2 inhibitors with improved aqueous solubility. Derivatives of 8-bromo-1,2-dihydro-3H-naphth[1,2-e][1,3]oxazine-3-thione N-alkylated w...

An entry from the Cambridge Structural Database, the world's repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

The  histone  deaceylases  SIRT4,  and  SIRT5  are  mitochondrial  proteins 
and  are  considered  as  metabolic  sensors  of  cell’s  energetic  status.  The 
two  enzymes  have  important  role  in  several  human  diseases  such  as 
cancer,  and  diabetes.  SIRT4  regulates  the  glutamate  dehydrogenase 
activity  and  insulin  secretion,  SIRT4  also  functions  as  a  cellular  lipoami-
dase  that  regulates  the  pyruvate  dehydrogenase  (PDH),  Its  catalytic 
efficiency  for  lipoyl  and  biotinyl  lysine  modifications  is  superior  to  its 
deacetylation  activity  [1–3]  whereas  SIRT5  removes  post-translational 
modifications  such  as  lysine  malonylation  and  succinylation  [4].  Recent 
studies reported that SIRT4 seems to have a tumor-suppressive function
[5,6] and may serve as a novel therapeutic target in colorectal cancer [7].
SIRT5 regulates urea production, reactive oxygen species (ROS) metabo
-
lism, via regulating the carbamoyl phosphate synthetase (CPS1) [3].
Due  to  the  absence  of  a  crystal  structure  for  human  SIRT4,  a  homol-
ogy  model  was  generated  using  different  templates  and  computa-
tional  approaches.  The  template  selection  identified  human  SIRT5  as 
most suitable template. MD simulations were carried out on the SIRT4
models  in  complex  with  the  cofactor  and  different  substrates  using 
program  AMBER  12  to  understand  the  stability  and  conformational 
changes  of  the  modeled  proteins  in  holo  and  apo  form.  In  addition, 
several MD simulations of available crystal structures of SIRT5 in com-
plex  and  in  apo  form  have  been  performed  and  compared  with  the 
results  obtained  for  SIRT4.  In  addition,  shape-based  virtual  screening 
for inhibitors and activators have been carried o

ABSTRACT
A reverse phase high performance liquid chromatography method was developed in this research for separation and assay of
antiprotozoal imidazole derivatives (Metronidazole, Tinidazole and Secnidazole). The separation was achieved by C8 column using
acetonitrite: water (20:80 v/v) as a mobile phase, a flow rate of 1.5 ml/min. UV detection was carried out at 318 nm. The retention
times of metronidazole, secnidazole and tinidazole were 4.140, 5.515 and 6.692 min respectively. The qualitative study of this
method included the effect of flow rate and the ratio of the components of mobile phase on the quality of separation. The method
was validated for accuracy, precision, selectivity and robustness. Linearity of metronidazole, secnidazole and tinidazole were in the
range of 80-120 μg/ml. The relative standard deviation for precision was not more than 2%. The recoveries in accuracy obtained for
metronidazole, secnidazole and tinidazole were 99.22%, 99.89 and 99.64% respectively. The developed method was found to be
rapid, accurate and precise and was used for the determination of the three compounds in raw materials and tablets. This method
was also used for the assay of these three compounds in the spiked human serum (1-30 μg/ml) and recoveries were in the range of
88-96%.
Keywords: RP-HPLC, Metronidazole, Tinidazole, Secnidazole.

Nonpolar derivatives of heterocyclic aromatic screening hits like the non-selective sirtuin inhibitor splitomicin tend to be poorly soluble in biological fluids. Unlike sp 3-rich natural products, flat aromatic compounds are prone to stacking and often difficult to optimize into leads with activity in cellular systems. The aim of this work was to identify anchor points for the introduction of sp 3-rich fragments with polar functional groups into the newly discovered active (IC 50 ¼ 5 mM) but nonpolar scaffold 1,2-dihydro-3H-naphth[1,2-e][1,3]oxazine-3-thione by a molecular modeling approach. Docking studies were conducted with structural data from crystallized human SIRT2 enzyme. Subsequent evaluation of the in silico hypotheses through synthesis and biological evaluation of the designed structures was accomplished with the aim to discover new SIRT2 inhibitors with improved aqueous solubility. Derivatives of 8-bromo-1,2-dihydro-3H-naphth[1,2-e][1,3]oxazine-3-thione N-alkylated with a hydrophilic morpholino-alkyl chain at the thiocarbamate group intended for binding in the acetyl-lysine pocket of the enzyme appeared to be promising. Both the sulfur of the thiocarbamate and the bromo substituent were assumed to result in favorable hydrophobic interactions and the basic morpholino-nitrogen was predicted to build a hydrogen bond with the backbone Ile196. While the brominated scaffold showed moderately improved activity (IC 50 ¼ 1.8 mM), none of the new compounds displayed submicromolar activity. Synthesis and characterization of the new compounds are reported and the possible reasons for the outcome are discussed.

The reversible acetylation of lysines is one of the best characterized epigenetic modifications. Its involvement in many key physiological and pathological processes has been documented in numerous studies. Lysine deacetylases (KDACs) and acetyltransferases (KATs) maintain the acetylation equilibrium at histones but also many other proteins. Besides acetylation, also other acyl groups are reversibly installed at the side chain of lysines in proteins. Because of their involvement in disease, KDACs and KATs were proposed to be promising drug targets, and for KDACs, indeed, five inhibitors are now approved for human use. While there is a similar level of evidence for the potential of KATs as drug targets, no inhibitor is in clinical trials. Here, we review the evidence for the diverse roles of KATs in disease pathology, provide an overview of structural features and the available modulators, including those targeting the bromodomains of KATs, and present an outlook.