wael rabeh - Academia.edu (original) (raw)

Papers by wael rabeh

Acta crystallographica. Section A, Foundations and advances, Aug 22, 2023

Ribokinase (RK) and ketohexokinase (KHK) are part of the phosphofructokinase B-type carbohydrate ... more Ribokinase (RK) and ketohexokinase (KHK) are part of the phosphofructokinase B-type carbohydrate kinase (PCK) family proteins. RK catalyzes the phosphorylation of ribose to ribose-5-phosphate (R5P) using ATP as phosphate donor. On the other hand, KHK uses ATP to phosphorylate fructose to fructose 1-phosphate (F1P). While fructose can be metabolized by hexokinase, most of the fructose is metabolized by KHK. Both kinases crystallize as a dimer in the asymmetric unit with the dimer formed through interactions between the two β-sheet from each monomer, forming a β-clasp domain (Fig. 1A). The enzyme possesses two domains, an N-terminal β-sheet domain and C-terminal α/β/α domain (Fig. 1B). The phosphorylation reactions for both kinases are initiated by an aspartate that acts as a general-base to deprotonate the O5'-hydroxyl group of ribose or the 1'-OH of fructose in RK and KHK, respectively (Fig. 2). Then the negatively charged O5' or O1' atoms nucleophilic attack the γ-phosphate of ATP.

Journal of Molecular Graphics and Modelling

Research Square (Research Square), Jul 15, 2020

Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) is responsible for the novel coronav... more Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) is responsible for the novel coronavirus disease 2019 (COVID-19). An appealing antiviral drug target is the coronavirus 3C-like protease (3CLpro) that is responsible for the processing of the viral polyproteins and liberation of functional proteins essential for the maturation and infectivity of the virus. In this study, multiple thermal analytical techniques have been implemented to acquire the thermodynamic parameters of 3CLpro at different buffer conditions. 3CLpro exhibited relatively high thermodynamic stabilities over a wide pH range; however, the protease was found to be less stable in the presence of salts. Divalent metal cations reduced the thermodynamic stability of 3CLpro more than monovalent cations; however, altering the ionic strength of the buffer solution did not alter the stability of 3CLpro. Furthermore, the most stable thermal kinetic stability of 3CLpro was recorded at pH 7.5, with the highest enthalpy of activation calculated from the slope of Eyring plot. The biochemical and biophysical properties of 3CLpro explored here will improve the solubility and stability of 3CLpro for optimum conditions for the setup of an enzymatic assay for the screening of inhibitors to be used as lead candidates in the drug discovery and antiviral design for therapeutics against COVID-19.

World Academy of Science, Engineering and Technology, International Journal of Chemical and Molecular Engineering, Aug 7, 2017

World Academy of Science, Engineering and Technology, International Journal of Biotechnology and Bioengineering, Mar 23, 2017

Adenylosuccinate lyase (ADSL) deficiency is a rare autosomal recessive disorder, which causes a d... more Adenylosuccinate lyase (ADSL) deficiency is a rare autosomal recessive disorder, which causes a defect in purine metabolism resulting in neurological and physiological symptoms. ADSL executes two nonsequential steps in the de novo synthesis of AMP: the conversion of phosphoribosylsuccinyl-aminoimidazole carboxamide (SAICAR) to phosphoribosylaminoimidazole carboxamide, which occurs in the de novo synthesis of IMP, and the conversion of adenylosuccinate to AMP, which occurs in the de novo synthesis of AMP and also in the purine nucleotide cycle, using the same active site. Mutation of ADSL's arginine 303 to a cysteine is known to lead to ADSL deficiency. Interestingly, unlike other mutations leading to ADSL deficiency, the R303C mutation has been suggested to more significantly affect the enzyme's ability to catalyze the conversion of succinyladenosine monophosphate than that of SAICAR to their respective products. To better understand the causation of disease due to the R303C mutation, as well as to gain insights into why the R303C mutation potentially has a disproportional decrease in activity toward its substrates, the wild type (WT) and the R303C mutant of ADSL were investigated enzymatically and thermodynamically. Additionally, the X-ray structures of ADSL in its apo form as well as with the R303C mutation were elucidated, providing insight into ADSL's cooperativity. By utilizing this information, a model for the interaction between ADSL and SAICAR is proposed.

Journal of Biological Chemistry, Feb 1, 2023

Biochemical Journal

The main protease of SARS-CoV-2, 3-chymotrypsin-like protease (3CLpro), is a prominent target for... more The main protease of SARS-CoV-2, 3-chymotrypsin-like protease (3CLpro), is a prominent target for antiviral development due to its essential role in the viral life cycle. Research has largely focused on competitive inhibitors of 3CLpro that target the active site. However, allosteric sites distal to the peptide substrate-binding region are also potential targets for the design of reversible noncompetitive inhibitors. Computational analyses have examined the importance of key contacts at allosteric sites of 3CLpro, but these contacts have not been validated experimentally. In this work, four druggable pockets spanning the surface of SARS-CoV-2 3CLpro were predicted: pocket 1 is the active site, whereas pockets 2, 3 and 4 are located away from the active site at the interface of domains II and III. Site-directed alanine mutagenesis of selected residues with important structural interactions revealed that 7 of 13 active site residues (N28, R40, Y54, S147, Y161, D187 and Q192) and 7 of ...

Molecules

The main protease enzyme (Mpro) of SARS-CoV-2 is one of the most promising targets for COVID-19 t... more The main protease enzyme (Mpro) of SARS-CoV-2 is one of the most promising targets for COVID-19 treatment. Accordingly, in this work, a structure-based virtual screening of 3.8 million ligand libraries was carried out. After rigorous filtering, docking, and post screening assessments, 78 compounds were selected for biological evaluation, 3 of which showed promising inhibition of the Mpro enzyme. The obtained hits (CB03, GR04, and GR20) had reasonable potencies with Ki values in the medium to high micromolar range. Interestingly, while our most potent hit, GR20, was suggested to act via a reversible covalent mechanism, GR04 was confirmed as a noncompetitive inhibitor that seems to be one of a kind when compared to the other allosteric inhibitors discovered so far. Moreover, all three compounds have small sizes (~300 Da) with interesting fittings in their relevant binding sites, and they possess lead-like characteristics that can introduce them as very attractive candidates for the fu...

An entry from the Cambridge Structural Database, the world's repository for small molecule cr... more 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.

Acta Crystallographica Section A Foundations and Advances, 2019

The different colors of light emitted by bioluminescent beetles ranging from yellow-green to red ... more The different colors of light emitted by bioluminescent beetles ranging from yellow-green to red are related to slightly different enzymes (luciferases) that catalyze the same two-stage chemical reaction, conversion of luciferin to oxyluciferin in presence of ATP and oxygen. However, luciferases with known crystal structures emit only green light with several mutations resulted in red emission (l max 610 nm) that is still far from the emission of the only red-emitting beetle luciferases (623 nm) from Phrixothrix hirtus (RE Ph). To shed light on the mechanism of color "tuning" in beetle luciferases, we determined the crystal structure of RE Ph in addition to a blue-shifted greenemitting luciferase from the firefly Amydetes vivianii (GB Av). The structure of RE Ph was found to be an oligomer with monomers with a/b structural fold, similar to other known luciferase structures. The active site is located between the large N-terminal and small C-terminal domains, where it opens or closes by motion of the latter. Multiple mutations were introduced in two loops to evaluate their roles in the emission color. First, loop at the bottom of the active site was found to have an effect on the energy of the emitted light. However, loop contains amino acids that affected emission of the RE Ph and GB Av luciferases.

Chemistry - A European Journal, Oct 12, 2017

Journal of Applied Crystallography, 2018

The research-driven laboratory experiment described herein has at its core the individual develop... more The research-driven laboratory experiment described herein has at its core the individual development of students, combining core subject matter with the opportunity to explore, in a research environment, areas outside of traditional curricula; however, it maintains the pedagogical training for an undergraduate major degree in chemistry and sciences in general. The laboratory can feasibly be implemented in high schools to expose students to an engaging and intellectually fulfilling aspect of chemistry early in their career. This seven-week project is based on the growth and study of crystals and encourages students, from the outset, to conceive, propose, design, plan and carry out their own research on chemicals and conditions of their own choosing. The wide array of laboratory equipment, analytical instrumentation and techniques that the students are potentially exposed to, from micropipettes and optical microscopes to scanning electron microscopy and powder X-ray diffraction, puts...

Molecular Cancer Research, 2016

Cancer utilizes glucose at elevated levels to support its growth and proliferation, historically ... more Cancer utilizes glucose at elevated levels to support its growth and proliferation, historically known as “ Warburg effect”. Targeting glucose metabolism in cancer cells to limit its growth will enhance patients' survival rate. Hexokinase catalyzes glucose phosphorylation, and is a major step in regulation of glycolysis. Four isozymes are present in human with Hexokinase 2 (HK2) being the most active and specifically expressed in verity of different cancers. In addition, gene expression profiling experiments of different types of cancer showed high expression levels of HK2, and various biological studies highlighted the importance of HK2 in tumor metastasis making it an ideal target to characterize cancer metabolism and for the development of new class of cancer therapeutics. We solved the crystal structure of human HK2 in complex with glucose and glucose-6-phosphate (PDB code: 2NZT), where it is a homodimer with catalytically active N- and C-terminal domains linked by a seven-t...

Biophysical Journal, 2016