Molecular Biophysical Sciences

Molecular Biophysical Sciences

From Molecular Structure to Biological Function

Morad Mustafa

Associate Professor of Computational Biophysical Chemistry

Photo: Morad Mustafa

Morad Mustafa

Associate Professor of Computational Biophysical Chemistry
Affiliation
Al-Zaytoonah University of Jordan, Amman, Jordan
Education

  • Ph.D., Computational Biophysical Chemistry, Brigham Young University, USA
  • M.S. (First Class Honors), Physical Chemistry, Yarmouk University, Jordan
  • B.S. (First Class Honors), Chemistry, Yarmouk University, Jordan
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Academic Biography

Education

Dr. Morad Mustafa earned a B.S. in Chemistry (1998) and an M.S. in Physical Chemistry (2001) from Yarmouk University, Jordan. He completed his Ph.D. at Brigham Young University, USA (2003–2008) specializing in computational biophysical chemistry and the study of biological systems.

Postdoctoral Training

Following his Ph.D., Dr. Morad Mustafa completed postdoctoral research at the University of Georgia, USA (2009–2010), where he used molecular dynamics simulations to study biological systems, including the Epidermal Growth Factor Receptor (EGFR).

Academic Appointments

In 2010, Dr. Morad Mustafa joined King Khalid University, Saudi Arabia, as an Assistant Professor of Computational Biophysical Chemistry. In 2022, he joined Al-Zaytoonah University of Jordan, Amman, as an Assistant Professor in the Department of Pharmacy. In 2026, he was promoted to Associate Professor of Computational Biophysical Chemistry at Al-Zaytoonah University of Jordan.

Research Focus

His research focuses on computational studies of biomolecular systems using advanced techniques, including Gaussian accelerated Molecular Dynamics (GaMD) simulations, Ligand Gaussian accelerated Molecular Dynamics (LiGaMD) simulations, and virtual screening. His work aims to understand protein structure–function relationships and identify potential lead compounds, particularly for cancer treatment.

Research Interests

Research Interest
  • Computational Drug Discovery
  • Molecular Dynamics Simulations
  • Computational Cancer Biology
  • Protein–Ligand Interactions

Understanding the functions of macromolecules, their interactions with cellular components, and the mechanisms that regulate these interactions remains a major challenge for both theoreticians and experimentalists. Gaining deeper insight into these functions, interactions, dynamics, and regulatory processes has broad applications across multiple disciplines, including structural biology, pharmacology, and medicine.

Dr. Morad Mustafa's research aims to advance our understanding of some of the most challenging cancers, particularly breast and lung cancers. To achieve this, he investigates biologically relevant molecular systems using state-of-the-art computational chemistry techniques, including molecular dynamics simulations and computer-aided drug discovery.

Dr. Morad Mustafa's current research focuses on elucidating the molecular mechanisms underlying breast and lung cancers by investigating key mutations that drive disease progression. He employs Gaussian Accelerated Molecular Dynamics (GaMD) and Ligand Gaussian accelerated Molecular Dynamics (LiGaMD) simulations to characterize the dynamic behavior of proteins encoded by the most frequently mutated genes in these cancers, enabling the capture of rare conformational transitions and protein–ligand interactions.

In parallel, his research integrates virtual screening of natural product libraries to identify promising inhibitors capable of modulating aberrant protein function. By combining advanced molecular simulations with computational drug discovery, his work seeks to identify novel therapeutic candidates with improved binding affinity and specificity, ultimately contributing to the development of more effective cancer treatments.

Publications

Member Publications

Peer-Reviewed Articles

  1. Taher, Deeb; Khalil, Belal; AlNaimat, Sara; Mustafa, Morad; Ishtaiwi, Zakariyya; Helal, Wissam; Korb, Marcus; Abu Thiab, Tuqa; Imraish, Amer; Alhindi, Tareq; Makahleh, Ahmad; Amer, Mohammad W.; and Duha H. Abdelrahman,. Synthesis, structural characterization and molecular docking analysis of novel β-ketoiminato palladium(ii) complexes with anticancer properties. RSC Advances. 2026; 25:22352–22367. https://doi.org/10.1039/D5RA09325B
  2. Oh, Yujeong; Palanikumar, L.; Howarth, Madeline; Maity, Debabrata; Ali, Liaqat; Mustafa, Morad; Kumar, Sunil; Hamilton, Andrew D.; Magzoub, Mazin. Prion Protein-Derived Cell-Penetrating Peptide Inhibits Type II Diabetes-Associated Islet Amyloid Polypeptide Aggregation and Cytotoxicity. Biochemistry. 2026; 65(8):1249–1260. https://doi.org/10.1021/acs.biochem.5c00634
  3. Gharaibeh, Mohammed; Al-Shami, Bayenah; Helal, Wissam; Mustafa, Morad. Vibrational energy level scheme of the BCH radical: A theoretical study of Renner-teller coupling. Computational and Theoretical Chemistry. 2026; 1261:115821. https://doi.org/10.1016/j.comptc.2026.115821
  4. Mustafa, Morad; Alwahsh, Mohammad; Hamadneh, Lama; Hasan, Aya; Abu-Irmaileh, Bashaer. Integrated virtual and experimental screening of natural products as potential anticancer agents against breast cancer. Bioorganic Chemistry. 2025; 166:109165. https://linkinghub.elsevier.com/retrieve/pii/S0045206825010454
  5. Taher, Deeb; Saleh, Sundus; Habashneh, Almeqdad Y.; Hourani, Wafa; Mustafa, Morad; Helal, Wissam; Al-Noaimi, Mousa; Obeidat, Safwan M.; Kloda, Matous; Alhindi, Tareq; Kailani, Mohammed H.; Ghazzy, Asma. Synthesis and anticancer activity of bis(β-ketoiminato) palladium(II) complexes of 3-[(chloro-substituted phenyl)amino]-1-phenyl-2-buten-1-one. Journal of Molecular Structure. 2025; 1340:142542. https://linkinghub.elsevier.com/retrieve/pii/S0022286025012219
  6. Taher, Deeb; Al-Said, Naim.H.; Albanna, Mohammad; Kloda, Matous; Mustafa, Morad; Helal, Wissam; Assaf, Khaleel I.; Hourani, Wafa; Kotob, Wael-Rémy; Saleh, Sundus; Makahleh, Ahmad;Rabba’a, Manar Mohammad. Biological activity evaluation and molecular docking studies of newly synthesized β-ketoiminato-based palladium complexes. Inorganica Chimica Acta. 2025; 583:122711. https://linkinghub.elsevier.com/retrieve/pii/S002016932500177X
  7. 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://portlandpress.com/biochemj/article/480/11/791/233103/Key-allosteric-and-active-site-residues-of-SARS
  8. 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://linkinghub.elsevier.com/retrieve/pii/S240584402204018X
  9. 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://link.springer.com/article/10.1134/S0036024422070251?error=cookies_not_supported&code=f60c7c7e-366f-43b0-a287-541b7dc43f02
  10. 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://link.springer.com/article/10.1007/s10930-022-10041-0?error=cookies_not_supported&code=29de6ac5-2f13-4dca-8ec1-7db66cf24b2b
  11. 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.
  12. 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://onlinelibrary.wiley.com/doi/10.1002/prot.22862
  13. 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://journals.plos.org/plosone/article?id=10.1371/journal.pone.0014310
  14. 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://onlinelibrary.wiley.com/doi/10.1002/prot.22376
  15. 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://linkinghub.elsevier.com/retrieve/pii/S0005273609001096
  16. 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://link.springer.com/article/10.1007/s12539-009-0025-3?error=cookies_not_supported&code=ae69527f-50a6-4ceb-aa79-7d8279a575ab
  17. 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://www.tandfonline.com/doi/abs/10.1080/00268970902852665
  18. 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://www.tandfonline.com/doi/abs/10.1080/08927020701654635
  19. 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://www.tandfonline.com/doi/abs/10.1080/00268970802116906
  20. 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.
  21. 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.
  22. 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://www.tandfonline.com/doi/abs/10.1080/00268970701355795
  23. 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://www.tandfonline.com/doi/abs/10.1080/08927020601054068

Conferences, Symposiums, and Workshops

  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. [Talk]
  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. [Talk]
  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. [Talk]
  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. [Talk]
  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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