Computational Biophysical Chemistry

Computational Biophysical Chemistry

Molecular Dynamics Simulations - Drug Discovery and Design - Biophysical Chemistry - Quantum Chemistry
Morad Mustafa

Morad Mustafa

Assistant Professor of Computational Biophysical Chemistry
Affiliation: Al-Zaytoonah University of Jordan, Amman, Jordan
Education:
* PhD, Computational Biophysical Chemistry, Brigham Young University, USA
* MS (First Class Honors), Physical Chemistry, Yarmouk University, Jordan
* BS (First Class Honors), Chemistry, Yarmouk University, Jordan
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Curriculum Vitae: Download

Academic Biography

 I graduated with a BS degree in Chemistry from Yarmouk University in Irbid, Jordan, in 1998. From 2003 to 2008, I completed my PhD studies at Brigham Young University in Utah, USA, under the supervision of Prof. Douglas J. Henderson and Prof. David D. Busath, focusing on the study of biological systems through computational biophysical chemistry methods.

From 2009 to 2010, I conducted my postdoctoral studies at the University of Georgia in Athens, USA, with Prof. Natarajan Kannan. There, I studied biological systems, including the Epidermal Growth Factor Receptor (EGFR), using molecular dynamics simulations. In 2010, I joined King Khalid University in Saudi Arabia as an assistant professor in the Department of Chemistry.

 In 2022, I became an Assistant Professor of Computational Biophysical Chemistry in the Department of Pharmacy at Al-Zaytoonah University of Jordan in Amman, Jordan. My research focuses on the study of biomolecular systems, including p53, urease, and aldehyde dehydrogenase (ALDH) proteins, using various computational techniques such as Gaussian accelerated Molecular Dynamics (GaMD), virtual screening, and Density Functional Theory (DFT). I am particularly interested in understanding protein structure-function relationships and in searching for lead compounds for treating several diseases, primarily cancer.

Research Interest

Research Areas: Molecular Dynamics Simulations, Virtual Screening, Density Functional Theory Calculations

Understanding the functions of macromolecules, as well as their interactions among cell components and how these interactions are regulated, challenges both theoreticians and experimentalists. A better understanding of those functions, interactions, dynamics, and regulations leads to many applications in different fields, such as structural biology, pharmacology, and medicine.

My research aims to explore and better understand some of the most pressing cancer diseases, such as breast and lung cancers. To this end, I conduct my research by studying modeled biological systems using cutting-edge computational chemistry methods, such as molecular dynamics simulations, drug discovery, and Density Functional Theory.

My current research project aims to illustrate the dynamical patterns of p53 forms, wild-type and mutants, by conducting molecular dynamics simulations. The targeted mutant forms include the top p53 mutants in lung and breast cancers. The impact of mutations on the dynamical patterns of wild-type p53 protein will be used in computer-aided drug design studies.

 

Publications

Peer-Reviewed Publications

  1. Al Adem, Kenana; Ferreira, Juliana C.; Fadl, Samar; Mustafa, Morad; and Rabeh, Wael M. Key Allosteric and Active Site Residues of SARS-CoV-2 3CLpro Are Promising Drug Targets. Biochemical Journal. 2023; 480(11):791–813. https://doi.org/10.1042/BCJ20230027
  2. Salman, Haya Ayyal; Yaakop, Amira Suriaty; Aladaileh, Saleem; Mustafa, Morad; Gharaibeh, Mohammed; Kahar, Ummirul Mukminin. Inhibitory effects of Ephedra alte on IL-10, IL-6, hybrid TLR4, TNF-α, IL-1β, and extracted TLR4 receptors: in silico molecular docking. Heliyon. 2023; 9(1):e12730. https://doi.org/10.1016/j.heliyon.2022.e12730
  3. Jamhour, Rasheed M. A. Q.; Al-Nadaf, Afaf H.; Wedian, Fadel; Al-Mazaideh, Ghassab M.; Mustafa, Morad; Huneif, Mohammed Ayed; Mahmoud, Sabry Younis; Farrag, Eman Saleh; Al-Rimawi, Fuad; Salman, Haya Ayyal; Alqudah, Ali Abdallah; Alakhras, Fadi. Phytochemicals as a potential inhibitor of COVID-19: An in silico perspective. Russian Journal of Physical Chemistry A. 2022; 96:1589–1597. https://doi.org/10.1134/S0036024422070251
  4. Mustafa, Morad; Gharaibeh, Mohammad. Most Probable Druggable Pockets in Mutant p53-Arg175His Clusters Extracted from Gaussian Accelerated Molecular Dynamics Simulations. Protein Journal. 2022; 41:27–43. https://doi.org/10.1007/s10930-022-10041-0
  5. Mustafa, Morad; Wedian, Fadel; Aldal’in, Hammad K.; Al-Mazaideh, Ghassab M.; Mahmoud, Sabry Younis; Farrag, Eman Saleh; Gharaibeh, Mohammed; Hijawi, Thameen; Al-Rimawi, Fuad; Abbadi, Jehad; Shalayel, Mohammed Helmy Faris; Siddique, Nadeem A.; Salman, Haya Ayyal; Huneif, Mohammed Ayed. The efficiency of some active ingredients of Arum Palaestina as inhibitors to 3CLpro and Nsp15 proteins. Acta Poloniae Pharmaceutica – Drug Research. 2021;78(5):657–665.
  6. Mustafa, Morad; Mirza, Amar; Kannan, Natarajan. Conformational regulation of the EGFR kinase core by the juxtamembrane and C-terminal tail: a molecular dynamics study. Proteins. 2011;79(1):99–114. https://doi.org/10.1002/prot.22862
  7. Mirza, Amar; Mustafa, Morad; Talevich, Eric; Kannan, Natarajan. Co-conserved features associated with cis regulation of ErbB tyrosine kinases. PLoS One. 2010;5(12):e14310. https://doi.org/10.1371/journal.pone.0014310
  8. Mustafa, Morad; Henderson, Douglas J.; Busath, David D. Free-energy profiles for ions in the influenza M2-TMD channel. Proteins. 2009;76(4):794–807. https://doi.org/10.1002/prot.22376
  9. Mustafa, Morad; Henderson, Douglas J.; Busath, David D. Computational studies of gramicidin permeation: an entryway sulfonate enhances cation occupancy at entry sites. Biochimica et Biophysica Acta – Biomembranes. 2009;1788(6):1404–1412. https://doi.org/10.1016/j.bbamem.2009.03.021
  10. Mustafa, Morad; Busath, David D. The gramicidin channel ion permeation free-energy profile: direct and indirect effects of CHARMM force field improvements. Interdisciplinary Sciences: Computational Life Sciences. 2009;1(2):113–127. https://doi.org/10.1007/s12539-009-0025-3
  11. Santos, Andrés; Yuste, Santos B.; López de Haro, Mariano; Alawneh, Morad; Henderson, Douglas. Contact values for disparate-size hard-sphere mixtures. Molecular Physics. 2009;107(7):685–691. https://doi.org/10.1080/00268970902852665
  12. Alawneh, Morad; Henderson, Douglas; Outhwaite, Christopher W.; Bhuiyan, Lutful Bari. The effect of dielectric polarization of the electrode on anomalous temperature effects in the electrical double layer. Molecular Simulation. 2008;34(5):501–507. https://doi.org/10.1080/08927020701654635
  13. Alawneh, Morad; Henderson, Douglas J. Molecular dynamics results for the radial distribution functions of highly asymmetric hard sphere mixtures. Molecular Physics. 2008;106(5):607–614. https://doi.org/10.1080/00268970802116906
  14. Bhuiyan, Lutful Bari; Outhwaite, Christopher W.; Henderson, Douglas; Alawneh, Morad. A further Monte Carlo and modified poisson-boltzmann analysis of two recent results in the electric double layer theory. Bangladesh Journal of Physics. 2007;4:93–102.
  15. Henderson, Douglas; Alawneh, Morad; Saavedra-Barrera, Rafael; Lozada-Cassou, Marcelo. Application of a recently proposed test to the hypernetted chain approximation for the electric double layer. Condensed Matter Physics. 2007;10(3(51)):323–330.
  16. Bhuiyan, Lutful Bari; Outhwaite, Christopher W.; Henderson, Douglas; Alawneh, Morad. A modified poisson-boltzmann theory and Monte Carlo simulation study of surface polarization effects in the planar diffuse double layer. Molecular Physics. 2007;105(10):1395–1402. https://doi.org/10.1080/00268970701355795
  17. Alawneh, Morad; Henderson, Douglas. Monte Carlo simulation of the double layer at an electrode including the effect of a dielectric boundary. Molecular Simulation. 2007;33(6):541–547. https://doi.org/10.1080/08927020601054068

Conferences and Symposiums

  1. Mustafa, Morad; Mirza, Amar; Kannan, Natarajan. The structural impact of cancer mutations in EGFR using molecular dynamics simulations. Georgia Cancer Research Symposium. Nov 5–6, 2008; Athens, GA, USA. [Poster]
  2. Mustafa, Morad; Busath, David D. Molecular dynamics simulations of Na+ transport free-energy profile for gramicidin and two analogs. Joint Northwest and Rocky Mountain Regional Meeting of the American Chemical Society. Jun 15–18, 2008; Park City, UT, USA. [Presentation]
  3. Mustafa, Morad; Henderson, Douglas J.; Busath, David D. CMAP helps solve the gramicidin problem. Biophysical Society (52nd Annual Meeting). Feb 2–6, 2008. Long Beach, CA, USA. [Poster]
  4. Mustafa, Morad; Henderson, Douglas J.; Busath, David D. A comparative study of force fields for tryptophan with experiment using MD simulations. Telluride Science Research Center (Ion Channel Biophysics). Jul 30–Aug 3, 2007. Telluride, CO, USA. [Presentation]
  5. Mustafa, Morad; Henderson, Douglas J.; Busath, David D. Studying the influenza M2 channel occupancy by other ions using MD simulations. Telluride Science Research Center (Ion Channel Biophysics). Jul 30–Aug 3, 2007. Telluride, CO, USA. [Presentation]
  6. Mustafa, Morad; Henderson, Douglas J.; Busath, David D. MD simulations of influenza M2 using different cation sizes in a lipid bilayer. Biophysical Society (51st Annual Meeting). Mar 3–7, 2007. Baltimore, MD, USA. [Presentation]
  7. Mustafa, Morad; Henderson, Douglas J.; Busath, David D. MD simulations of gramicidin A and taurine gramicidin A in a lipid bilayer. Biophysical Society (51st Annual Meeting). Mar 3–7, 2007. Baltimore, MD, USA. [Poster]

Non-Refereed Publications

  1. Mustafa, Morad. Ion permeation through membrane channels: molecular dynamics simulations studies. Brigham Young University Dissertation. Advisers: Prof Douglas J. Henderson and Prof David D. Busath.
  2. Mustafa, Morad. The role of cyclodextrin cavity size on the normal and twisted intramolecular charge transfer (TICT) fluorescence of N,N-disubstituted p-cyanoanilines in aqueous solutions. Yarmouk University Thesis. Adviser: Prof Khader Al-Hassan.
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