Gustavo Seabra

Gustavo Seabra, Ph.D.

Research Associate Professor

Department: Medicinal Chemistry
Business Phone: (352) 273-7714
Business Email: seabra@cop.ufl.edu

About Gustavo Seabra

Gustavo received his Ph.D. from the Chemistry Department of Kansas State University in 2005 in prof. J. Vincent Ortiz group (now at Auburn University), working with development and applications of quantum mechanical methods for accurately predicting molecular photoionization spectra. He then moved to University of Florida, Gainesville, for a postdoc in the Quantum Theory Project with Prof. Adrian Roitberg from the Chemistry Department, working on implementation of hybrid quantum mechanical / molecular mechanics (QM/MM) methods for simulating chemical reactions in complex environments such as enzymes or solutions, allowing the understanding of the molecular mechanism of such reactions and explore new drug candidates as transition state analogues. After the postdoc, he was hired by the Federal University in Pernambuco, in Brazil, where he worked as a Chemistry Professor and applied those techniques to enzymes related to Alzheimer’s disease, and the Dengue and Zika viruses, along with docking techniques to understand the interactions between small molecule inhibitors and their respective enzyme receptors, and virtual high-throughput screening to find new drug candidates against Dengue virus. In 2019 he was hired back by University of Florida. He is now a research associate professor in the College of Pharmacy, in the Department of Medicinal Chemistry and the Center for Natural Products, Drug Discovery and Development (CNPD3), contributing with molecular modeling expertise to the drug discovery projects.

Teaching Profile

Courses Taught
2007-2008
CHM3400 Physical Chemistry for the Biosciences
2021
PHA6935 Selected Topics in Pharmacy
2022
PHA6467C Drug Design II

Research Profile

Development and application to drug discovery of diverse computational chemistry methods, including Quantum Chemistry, Molecular Dynamics, hybrid multi-scale (QM/MM) simulations of reactions, Docking and Scoring and Virtual High Throughput Screening, and machine learning methods.

Areas of Interest
  • Artificial Intelligence
  • Computational Chemistry
  • Machine Learning
Open Researcher and Contributor ID (ORCID)

0000–000-2-13-03-4-483

Publications

2022
Diversity and Chemical Library Networks of Large Data Sets
Journal of Chemical Information and Modeling. 62(9):2186-2201 [DOI] 10.1021/acs.jcim.1c01013.
2021
Bifunctional Doscadenamides Activate Quorum Sensing in Gram-Negative Bacteria and Synergize with TRAIL to Induce Apoptosis in Cancer Cells
Journal of Natural Products. 84(3):779-789 [DOI] 10.1021/acs.jnatprod.0c01003. [PMID] 33480689.
2021
Binding Mechanism between Acetylcholinesterase and Drugs Pazopanib and Lapatinib: Biochemical and Biophysical Studies
ACS Chemical Neuroscience. 12(24):4500-4511 [DOI] 10.1021/acschemneuro.1c00521.
2021
Effects of pyriproxyfen on zebrafish brain mitochondria and acetylcholinesterase
Chemosphere. 263 [DOI] 10.1016/j.chemosphere.2020.128029.
2021
Impact on cholinesterase-inhibition and in silico investigations of sesquiterpenoids from Amazonian Siparuna guianensis Aubl.
Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy. 252 [DOI] 10.1016/j.saa.2021.119511.
2021
Ultrasensitive small molecule fluorogenic probe for human heparanase
Chemical Science. 12(1):239-246 [DOI] 10.1039/d0sc04872k. [PMID] 34163592.
2020
Ahp-Cyclodepsipeptides as tunable inhibitors of human neutrophil elastase and kallikrein 7: Total synthesis of tutuilamide A, serine protease selectivity profile and comparison with lyngbyastatin 7.
Bioorganic & medicinal chemistry. 28(23) [DOI] 10.1016/j.bmc.2020.115756. [PMID] 33002682.
2020
Insights on the interaction of furfural derivatives with BSA and HTF by applying multi-spectroscopic and molecular docking approaches
Journal of Molecular Liquids. 317 [DOI] 10.1016/j.molliq.2020.114021.
2019
Design and Synthesis of Triazole-Phthalimide Hybrids with Anti-inflammatory Activity
Chemical and Pharmaceutical Bulletin. 67(2):96-105 [DOI] 10.1248/cpb.c18-00607.
2019
Furan inhibitory activity against tyrosinase and impact on B16F10 cell toxicity
International Journal of Biological Macromolecules. 136:1034-1041 [DOI] 10.1016/j.ijbiomac.2019.06.120.
2019
Spiro-acridine inhibiting tyrosinase enzyme: Kinetic, protein-ligand interaction and molecular docking studies
International Journal of Biological Macromolecules. 122:289-297 [DOI] 10.1016/j.ijbiomac.2018.10.175.
2018
Molecular dynamics simulations reveal the influence of dextran sulfate in nanoparticle formation with calcium alginate to encapsulate insulin
Journal of Biomolecular Structure and Dynamics. 36(5):1255-1260 [DOI] 10.1080/07391102.2017.1318305.
2018
Response to ‘On the antiviral activity and developmental toxicity of 6-methylmercaptopurine riboside (6MMPr)’ and ‘Acceleration with the brakes on?’
International Journal of Antimicrobial Agents. 52(4):515-516 [DOI] 10.1016/j.ijantimicag.2018.06.021.
2016
Reaction mechanism of the dengue virus serine protease: a QM/MM study
Physical Chemistry Chemical Physics. 18(44):30288-30296 [DOI] 10.1039/c6cp03209e.
2015
PUPIL: A Software Integration System for Multi-Scale QM/MM-MD Simulations and Its Application to Biomolecular Systems.
Advances in protein chemistry and structural biology. 100:1-31 [DOI] 10.1016/bs.apcsb.2015.06.002. [PMID] 26415839.
2015
QM/MM simulations of amyloid-β 42 degradation by IDE in the presence and absence of ATP.
Journal of chemical information and modeling. 55(1):72-83 [DOI] 10.1021/ci500544c. [PMID] 25539133.
2014
Molecular Dynamics Simulations Reveal a Novel Mechanism for ATP Inhibition of Insulin Degrading Enzyme
Journal of Chemical Information and Modeling. 54(5):1380-1390 [DOI] 10.1021/ci400695m.
2012
Comment on “A minimal implementation of the AMBER-GAUSSIAN interface for ab initio QM/MM-MD simulation”.
Journal of computational chemistry. 33(19):1643-4 [DOI] 10.1002/jcc.23003. [PMID] 22570199.
2009
A Multiscale Treatment of Angeli’s Salt Decomposition.
Journal of chemical theory and computation. 5(1):37-46 [DOI] 10.1021/ct800236d. [PMID] 26609819.
2009
Are current semiempirical methods better than force fields? A study from the thermodynamics perspective.
The journal of physical chemistry. A. 113(43):11938-48 [DOI] 10.1021/jp903474v. [PMID] 19848431.
2009
Mixed Quantum-Classical Calculations in Biological Systems
Challenges and Advances in Computational Chemistry and Physics. 3-20 [DOI] 10.1007/978-1-4020-9956-4_1.
2008
A versatile AMBER-Gaussian QM/MM interface through PUPIL.
Journal of computational chemistry. 29(10):1564-73 [DOI] 10.1002/jcc.20915. [PMID] 18270957.
2008
Quantifying Solvation Effects on Peptide Conformations: A QM/MM Replica Exchange Study
Challenges and Advances in Computational Chemistry and Physics. 507-518 [DOI] 10.1007/978-1-4020-8270-2_18.
2007
Chapter 6 Electronic structure and reactivity in double Rydberg anions: characterization of a novel kind of electron pair
Theoretical and Computational Chemistry. 87-100 [DOI] 10.1016/s1380-7323(07)80007-0.
2007
Implementation of the SCC-DFTB Method for Hybrid QM/MM Simulations within the Amber Molecular Dynamics Package†
The Journal of Physical Chemistry A. 111(26):5655-5664 [DOI] 10.1021/jp070071l. [PMID] 17521173.
2007
Mixed QM / MM Calculations in Biological Systems
Neumann Institute for Computing (NIC) Series. 36:37-43
2005
Molecular photoionization cross sections in electron propagator theory: Angular distributions beyond the dipole approximation
The Journal of Chemical Physics. 123(11) [DOI] 10.1063/1.2043087.
2004
Electron propagator theory calculations of molecular photoionization cross sections: The first-row hydrides
The Journal of Chemical Physics. 121(9):4143-4155 [DOI] 10.1063/1.1773135.
2002
Electron Propagator Theory of Ionization Energies and Dyson Orbitals for μ-Hydrido, Bridge-Bonded Molecules: Diborane, Digallane, and Gallaborane
ACS Symposium Series. 118-134 [DOI] 10.1021/bk-2002-0827.ch007.
2000
Synthesis and Antiinflammatory Activity of 3-Aryl-5-Isopropyl-1,2,4-Oxadiazoles
Heterocyclic Communications. 6(1):41-48 [DOI] 10.1515/HC.2000.6.1.41.
1997
Anomeric effect enhancement in C-5-substituted 2-methoxytetrahydropyrans
Journal of Molecular Structure. 412(1-2):51-58 [DOI] 10.1016/s0022-2860(97)00001-x.
1997
Preparation and reactions of 3-[3-(aryl)-1,2,4-oxadiazol-5-yl&#093: propionic acids
Journal of the Brazilian Chemical Society. 8(4):397-405 [DOI] 10.1590/s0103-50531997000400013.
1995
Theoretical study of the O4 molecule
Journal of Molecular Structure: THEOCHEM. 335(1-3):59-61 [DOI] 10.1016/0166-1280(94)03983-r.
Application and Testing of Diagonal, Partial Third-Order Electron Propagator Approximations
Understanding Chemical Reactivity. 131-160 [DOI] 10.1007/0-306-47632-0_5.

Grants

Jul 2021 ACTIVE
Novel Imine Formation by ATP Grasp Enzymes
Role: Co-Investigator
Funding: NATL SCIENCE FOU

Education

Ph.D. in Chemistry
2000-2005 · Kansas State University – Manhattan, KS – USA
M.Sc. in Chemistry
1996-1999 · Universidade Federal de Pernambuco – Recife, PE – Brazil
B.Sc. in Chemistry
1992-1996 · Universidade Federal de Pernambuco – Recife, PE – Brazil

Contact Details

Phones:
Business:
(352) 273-7714
Emails:
Business:
seabra@cop.ufl.edu
Addresses:
Business Mailing:
PO Box 100485
GAINESVILLE FL 32610
Business Street:
MSB P6-20
1345 CENTER DRIVE
GAINESVILLE FL 32610