Alexander MacKerell explained

Nationality:American
Grollman-Glick Professor of Pharmaceutical Sciences
Website:https://mackerell.umaryland.edu
Alma Mater:Rowan College of South Jersey
University of Hawaiʻi at Mānoa
Rutgers University
Doctoral Advisor:Regina Pietruszko
Academic Advisors:Rudolph Rigler
Martin Karplus
Discipline:Biochemistry
Biophysics
Workplaces:University of Maryland, Baltimore

Alexander D. MacKerell, Jr. is an American biophysicist who is the Grollman-Glick Professor of Pharmaceutical Sciences at the University of Maryland, Baltimore (UMB) and the Director of the Computer-Aided Drug Design (CADD) Center at UMB. He is also the Co-Founder and Chief Scientific Officer of the drug design tech company SilcsBio.[1] In 2022, MacKerell was awarded the prestigious American Chemical Society Award for Computers in Chemical and Pharmaceutical Research.[2] [3]

Education and early career

Alexander D. MacKerell, Jr. began his post-secondary education at Rowan College of South Jersey, then Gloucester County College.[4] He obtained an associate degree in biology in 1979, then a bachelor's degree in chemistry from the University of Hawaiʻi at Mānoa in 1981. MacKerell returned to New Jersey and enrolled at Rutgers University to work on a PhD under biochemist Regina Pietruszko, which he completed in 1985. MacKerell held a postdoctoral fellowship at the Karolinska Institute under Rudolf Rigler for two years before moving back to the US where he worked on the development of the CHARMM protein force field under Martin Karplus at Harvard University.[5] MacKerell held a one-year appointment as a Visiting assistant professor at Swarthmore College in 1992-93, before accepting a position at University of Maryland, Baltimore in the Department of Pharmaceutical Sciences.[6]

Research

MacKerell's research contributions have been primarily in the field of computational biophysics, using modeling and simulation techniques such as Molecular dynamics or Monte Carlo to study the structure, function, and dynamics of biological macromolecules such as proteins, nucleic acids and lipids. MacKerell has been a leading developer of the widely-used CHARMM all-atom additive force field, particularly on parameterization, expanding it from primarily proteins in water in the early 1990s to include lipids,[7] nucleic acids,[8] carbohydrates[9] and organic small molecules.[10] Alongside the lab of Benoit Roux, the MacKerell lab has led the development of the CHARMM-based Drude polarizable force field,[11] which aims to address a key limitation of additive force fields, namely that each atom gets a single, fixed partial charge regardless of local environment. The group has developed or contributed to the development of online tools to make academic research more straightforward and accessible. These include CGenFF,[12] [13] FFParam[14] and DGenFF[15] for automated generation of force field parameters for novel small molecules (such as drug-like molecules), and the CHARMM-GUI webserver[16] used to generate inputs for various simulations. Besides force field development, the MacKerell group has also contributed to computational drug design in the development of the Grand-canonical Monte Carlo/Molecular dynamics sampling method[17] upon which the Site-Identification by Ligand Competitive Saturation (SILCS)[18] technology is based. In 2008, he was named the inaugural Grollman-Glick Professor of Pharmaceutical Science at UMB.[19] [20] In 2022, the American Chemical Society awarded MacKerell the Award for Computers in Chemical and Pharmaceutical Research.

MacKerell serves as an editor of the Journal of Computational Chemistry[21] PLOS Computational Biology,[22] and .[23]

Awards and honors

External links

Notes and References

  1. Web site: fa-admin . 2022-12-14 . Alex MacKerell, PhD, SilcsBio Co-founder & CSO, Co-Leads Study on Use of SILCS Technology to Improve Lung Disease Treatments - SilcsBio Computer-Aided Drug Design . 2023-12-03 . SilcsBio . en-US.
  2. Web site: 2022 Recipients. ACS. Dec 2, 2023.
  3. Web site: News Center » MacKerell Honored with American Chemical Society Award . 2024-07-10 . en.
  4. Web site: MacKerell . Alex . Feb 7, 2024 . Curriculum Vitae of Alexander D. MacKerell, Jr. . Feb 7, 2024 . MacKerell Lab website.
  5. All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins . 10.1021/jp973084f . 1998 . MacKerell . A. D. . Bashford . D. . Bellott . M. . Dunbrack . R. L. . Evanseck . J. D. . Field . M. J. . Fischer . S. . Gao . J. . Guo . H. . Ha . S. . Joseph-Mccarthy . D. . Kuchnir . L. . Kuczera . K. . Lau . F. T. K. . Mattos . C. . Michnick . S. . Ngo . T. . Nguyen . D. T. . Prodhom . B. . Reiher . W. E. . Roux . B. . Schlenkrich . M. . Smith . J. C. . Stote . R. . Straub . J. . Watanabe . M. . Wiórkiewicz-Kuczera . J. . Yin . D. . Karplus . M. . The Journal of Physical Chemistry B . 102 . 18 . 3586–3616 . 24889800 .
  6. Web site: Alex MacKerell . 2024-01-04 . faculty.rx.umaryland.edu.
  7. Klauda . Jeffery B. . Venable . Richard M. . Freites . J. Alfredo . O’Connor . Joseph W. . Tobias . Douglas J. . Mondragon-Ramirez . Carlos . Vorobyov . Igor . MacKerell . Alexander D. . Pastor . Richard W. . 2010-06-17 . Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types . The Journal of Physical Chemistry B . en . 114 . 23 . 7830–7843 . 10.1021/jp101759q . 1520-6106 . 2922408 . 20496934.
  8. MacKerell . Alexander D. . Banavali . Nilesh . Foloppe . Nicolas . 2000 . Development and current status of the CHARMM force field for nucleic acids . Biopolymers . en . 56 . 4 . 257–265 . 10.1002/1097-0282(2000)56:4<257::AID-BIP10029>3.0.CO;2-W . 11754339 . 19502363 . 0006-3525.
  9. Guvench . Olgun . Mallajosyula . Sairam S. . Raman . E. Prabhu . Hatcher . Elizabeth . Vanommeslaeghe . Kenno . Foster . Theresa J. . Jamison . Francis W. . MacKerell . Alexander D. . 2011-10-11 . CHARMM Additive All-Atom Force Field for Carbohydrate Derivatives and Its Utility in Polysaccharide and Carbohydrate–Protein Modeling . Journal of Chemical Theory and Computation . en . 7 . 10 . 3162–3180 . 10.1021/ct200328p . 1549-9618 . 3224046 . 22125473.
  10. Vanommeslaeghe . K. . Hatcher . E. . Acharya . C. . Kundu . S. . Zhong . S. . Shim . J. . Darian . E. . Guvench . O. . Lopes . P. . Vorobyov . I. . Mackerell . A. D. . March 2010 . CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields . Journal of Computational Chemistry . en . 31 . 4 . 671–690 . 10.1002/jcc.21367 . 0192-8651 . 2888302 . 19575467.
  11. Web site: A simple polarizable model of water based on classical Drude oscillators . 2023-12-03 . pubs.aip.org.
  12. Vanommeslaeghe . K. . MacKerell . A. D. . 2012-12-21 . Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing . Journal of Chemical Information and Modeling . en . 52 . 12 . 3144–3154 . 10.1021/ci300363c . 1549-9596 . 3528824 . 23146088.
  13. Vanommeslaeghe . K. . Raman . E. Prabhu . MacKerell . A. D. . 2012-12-21 . Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges . Journal of Chemical Information and Modeling . en . 52 . 12 . 3155–3168 . 10.1021/ci3003649 . 1549-9596 . 3528813 . 23145473.
  14. Kumar . Anmol . Yoluk . Ozge . MacKerell . Alexander D. . 2020-04-05 . FFParam: Standalone package for CHARMM additive and Drude polarizable force field parametrization of small molecules . Journal of Computational Chemistry . en . 41 . 9 . 958–970 . 10.1002/jcc.26138 . 0192-8651 . 7323454 . 31886576.
  15. Kumar . Anmol . Pandey . Poonam . Chatterjee . Payal . MacKerell . Alexander D. . 2022-03-08 . Deep Neural Network Model to Predict the Electrostatic Parameters in the Polarizable Classical Drude Oscillator Force Field . Journal of Chemical Theory and Computation . en . 18 . 3 . 1711–1725 . 10.1021/acs.jctc.1c01166 . 1549-9618 . 8904317 . 35148088.
  16. Jo . Sunhwan . Cheng . Xi . Lee . Jumin . Kim . Seonghoon . Park . Sang-Jun . Patel . Dhilon S. . Beaven . Andrew H. . Lee . Kyu Il . Rui . Huan . Park . Soohyung . Lee . Hui Sun . Roux . Benoît . MacKerell . Alexander D. . Klauda . Jeffrey B. . Qi . Yifei . 2017-06-05 . CHARMM-GUI 10 years for biomolecular modeling and simulation . Journal of Computational Chemistry . en . 38 . 15 . 1114–1124 . 10.1002/jcc.24660 . 0192-8651 . 5403596 . 27862047.
  17. Guvench . Olgun . Jr . Alexander D. MacKerell . 2009-07-10 . Computational Fragment-Based Binding Site Identification by Ligand Competitive Saturation . PLOS Computational Biology . en . 5 . 7 . e1000435 . 10.1371/journal.pcbi.1000435 . 1553-7358 . 2700966 . 19593374 . free . 2009PLSCB...5E0435G .
  18. Web site: 2021-05-18 . SilcsBio - SilcsBio Computer-Aided Drug Design . 2023-12-03 . SilcsBio . en-US.
  19. Web site: News Center » First Grollman-Glick Professor Named . 2023-12-03 . en.
  20. Web site: Endowed Chairs . 2023-12-03 . www.pharmacy.umaryland.edu.
  21. Web site: Editorial board . Dec 3, 2023 . Journal of Computational Chemistry.
  22. Web site: PLOS Computational Biology . 2023-12-03 . journals.plos.org.
  23. Web site: Editorial board . Proteins: Structure, Function, & Bioinformatics.
  24. Web site: News Center » MacKerell selected "2006 Maryland Chemist of the Year" . 2023-12-03 . en.
  25. Web site: News Center » 2012 Researcher of the Year . 2023-12-03 . en.
  26. Web site: The Goodman Lecture. Oregon Health and Safety University. Dec 2, 2023.
  27. Web site: AWARDS. ISQBP. Dec 2, 2023.
  28. Web site: 2022 Recipients. ACS. Dec 2, 2023.

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