Faculty and Staff Biography

Muhammad Hagras

Education

• Doctor of Philosophy in Biophysics

University of California Davis

Advisor: Professor Alexei A. Stuchebrukhov

Dissertation: “Quantum Computational Studies of Electron Transfer in Respiratory Complex III and its Application for Designing New Mitocan Drugs”

• Master of Science in Chemical and Pharmaceutical Sciences

Advisor: Professor Jesika Faridi

Dissertation: “Overexpression of active AKT3 induces differential binding of co-regulator proteins to the estrogen receptor as a possible mechanism of Tamoxifen resistance.”

• Information Technology Diploma 2003

Information Technology Institute Cairo, Egypt

Training Courses include:

Software development using C/C++, .NET, and JAVA

Website design and development using ASP.NET and Javascript

Database development and administration of Oracle and SQL server

• Software Development Scholarship and Certificate

Information Technology ORASCOM Institute Cairo, Egypt

Training Courses include:

Microsoft SQL server development

Visual C++ desktop and distributed software development

• B.Sc. in Pharmaceutical and Clinical Sciences

Faculty of Pharmacy, Ain Shams University Cairo, Egypt

Specialty

Over the years, I acquired a unique combination of knowledge spanning different scientific fields, including quantum chemistry, biological, pharmaceutical, biophysical, and professional computer programming. All such knowledge and experience are integrated and continuously enhanced to achieve a robust scientific career. I am primarily interested in theoretical quantum chemistry in the general sense, with applications to biological systems and human health.

Current Research

My current research spans a multitude of interesting fields:

A. Development Side:

1- Development of an accurate and fast QM/MM-MD GPU-engine with a user-friendly interface

2- Development of various tools on top of the QM/MM-MD engine that will speed up the drug design process

B. Application Side:

1- Study the electron transfer process in the diffenet reaction center complexes using the QM/MM-MD method to better understand those processes. Such study can aid in better havesting solar energy and hence better designing new solar cells.

2- Drug design of new Mitocans against the newly discovered NQ site in the respiratory complex III. 

3- Study and designing of new anti-viral drugs against Covid-19 that acts by splitting very critical disulfide bonds in their "hooks".

Current Courses, Activities, and Scholarly Interest

I love to teach: Quantum chemistry, Physical chemistry, computational chemistry and general chemistry

Vita Highlights

WORK EXPERIENCE:

Massachusetts Institute of Technology Cambridge, MA

Postdoctoral Associate 

• Principal Investigator: Prof. Bernhardt L. Trout

Projects: In collaboration with Merck Sharp & Dohme Corp.

o Computational modeling of the disulfide crosslinking reaction with different oxidants.

o Development of novel ab-initio self-consistent QM/MM-MD method.

o Study of the micro-environmental effect on the disulfide crosslinking reaction.

Shanghai New York University Shanghai, China

Postdoctoral Associate

• Principal Investigator: Assistant Prof. William J. Glover

• Projects: Development of polarizable embedding QM/MM method.

University of California Davis, CA

Junior Specialist

• Principal Investigator: Prof. Alexei. A. Stuchebrukhov

• Projects: Study of the electron transfer currents in the respiratory complex I.

University of California Davis, CA

Teaching Assistant/Head TA

University of the Pacific Stockton, CA

Teaching Assistant

IBM Egypt Cairo, Egypt

Software Developer 2003-2004

• Projects:

o I have worked on the WBI Modeler using Visual C++ 6.

o I have worked on the WBI Monitor product using Java and Oracle/DB2.

ABSTRACTS, PUBLICATIONS, AND PATENTS:

Hagras MA, Marek RA, Feras Hatahet, and Trout BL. Computational Modeling for the Oxidation Reactions of the Cysteine Residues with the Superoxide and the Organic Radical Species. The Journal of Physical Chemistry A. (submitted and revised).

Hagras MA, Bellucci MA, Gobbo G, Marek RA, and Trout BL. Computational Modelling for the Disulfide Cross-linking Reaction. The Journal of Physical Chemistry B. 2020 Oct 28;124(44): 9840-9851.

Wang P, Dhananjayan N, Hagras MA, Stuchebrukhov AA. Respiratory complex I: Bottleneck at the entrance of quinone site requires conformational change for its opening. Biochimica et Biophysica Acta (BBA)-Bioenergetics. 2020 Oct 9:148326.

Hagras M, Stuchebrukhov A, inventors. Inhibition of respiratory complex III by ligands that interact with a regulatory switch. The United States patent application US 16/531,511. 2020 Jan 23.

Ni Y, Hagras MA, Konstantopoulou V, Mayr JA, Stuchebrukhov AA, Meierhofer D. Mutations in NDUFS1 Cause Metabolic Reprogramming and Disruption of the Electron Transfer. Cells. 2019 Oct;8(10):1149.

Hagras MA*, Stuchebrukhov AA*. Concerted Two-Electron Reduction of Ubiquinone in Respiratory Complex I. The Journal of Physical Chemistry B. 2019 May 29;123(25):5265-73.

Hagras MA, Glover WJ. Polarizable Embedding for Excited-State Reactions: Dynamically Weighted Polarizable QM/MM. Journal of chemical theory and computation. 2018 Mar 21;14(4):2137-44.

Stuchebrukhov AA, Hagras MA. Two-electron reduction of ubiquinone in respiratory complex I. Biochimica et Biophysica Acta (BBA)-Bioenergetics. 2018 Sep 1;1859:e43.

Hagras MA, Stuchebrukhov AA. Electron tunneling in proteins program. Journal of Computational Chemistry. 2016 Jun 5;37(15):1388-95.

Hagras MA, Stuchebrukhov AA., Internal switches modulating electron tunneling currents in respiratory complex III, Biochim Biophys Acta. 2016 Jun;1857(6):749-758.

Hagras MA, Stuchebrukhov AA., Novel Inhibitors for a Novel Binding Site in Respiratory Complex III, J Phys Chem B. 2016 Mar 17;120(10):2701-8.

Hagras MA, Hayashi T, Stuchebrukhov AA., Quantum Calculations of Electron Tunneling in Respiratory Complex III, The Journal of Physical Chemistry B 2015 119 (46), pp 14637-51.

Hagras MA, Stuchebrukhov AA., Transition Flux Formula for the Electronic Coupling Matrix Element, The journal of physical chemistry. B, 2015, 119 (24), pp 7712–7721.

Hagras, M., Hayashi, T., Stuchebrukhov, A. (Sep., 2015). Computational studies of electron tunneling in respiratory complex III. Combined Biology Program Training Grant Retreat.

Hagras, M., Stuchebrukhov, A. (Feb. 2015). Internal switches modulating electron flow in bc1 complex. Biophysical Society 59th Annual Meeting.

Hagras, M., Hayashi, T., Stuchebrukhov, A. (Feb. 2014). Computational studies of electron tunneling in respiratory complex III. Biophysical Society 58th Annual Meeting.

Hagras, M., Faridi, J.S. (May 2008). Overexpression of active Akt3 induces differential binding of co-regulator proteins to the estrogen receptor as a possible mechanism of tamoxifen resistance. American Association for Cancer Research.

Interesting Facts

If you are interested to learn more about my research and to join my group, you can visit my research site: www.infiniquantum.com

And you can email me at: muhammad.hagras@uhsp.edu