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Research Output 1985 2019

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10 Citations (Scopus)

4 Molecular Modeling of Opioid Receptor-Ligand Complexes

McFadyen, I., Metzger, T., Subramanian, G., Poda, G., Jorvig, E. & Ferguson, D. M., Jan 1 2002, In : Progress in Medicinal Chemistry. 40, C, p. 107-135 29 p.

Research output: Contribution to journalArticle

10 Citations (Scopus)

9-Amino acridine pharmacokinetics, brain distribution, and in vitro/in vivo efficacy against malignant glioma

Teitelbaum, A. M., Gallardo, J. L., Bedi, J., Giri, R., Benoit, A. R., Olin, M. R., Morizio, K. M., Ohlfest, J. R., Remmel, R. P. & Ferguson, D. M., Jun 1 2012, In : Cancer chemotherapy and pharmacology. 69, 6, p. 1519-1527 9 p.

Research output: Contribution to journalArticle

Acridines
Pharmacokinetics
Glioma
Brain
Biological Availability
9 Citations (Scopus)

Acidic pH-responsive polymer nanoparticles as a TLR7/8 agonist delivery platform for cancer immunotherapy

Kim, H., Sehgal, D., Kucaba, T. A., Ferguson, D. M., Griffith, T. S. & Panyam, J., Nov 28 2018, In : Nanoscale. 10, 44, p. 20851-20862 12 p.

Research output: Contribution to journalArticle

Polymers
Nanoparticles
T-cells
Gases
Antigens
1 Citation (Scopus)

A Cinchona Alkaloid Antibiotic That Appears to Target ATP Synthase in Streptococcus pneumoniae

Wang, X., Zeng, Y., Sheng, L., Larson, P., Liu, X., Zou, X., Wang, S., Guo, K., Ma, C., Zhang, G., Cui, H., Ferguson, D. M., Li, Y., Zhang, J. & Aldrich, C. C., Mar 14 2019, In : Journal of Medicinal Chemistry. 62, 5, p. 2305-2332 28 p.

Research output: Contribution to journalArticle

Cinchona Alkaloids
Quinuclidines
Streptococcus pneumoniae
Adenosine Triphosphate
Anti-Bacterial Agents
39 Citations (Scopus)
salvinorin A
kappa Opioid Receptor
Drug Design
G-Protein-Coupled Receptors
drugs
21 Citations (Scopus)

A computational analysis of interaction energies in methane and neopentane dimer systems

Metzger, T. G., Ferguson, D. M. & Glauser, W. A., Jan 15 1997, In : Journal of Computational Chemistry. 18, 1, p. 70-79 10 p.

Research output: Contribution to journalArticle

Computational Analysis
Methane
Dimer
Dimers
Energy
87 Citations (Scopus)

Acridine-based agents with topoisomerase II activity inhibit pancreatic cancer cell proliferation and induce apoptosis

Goodell, J. R., Ougolkov, A. V., Hiasa, H., Kaur, H., Remmel, R. P., Billadeau, D. D. & Ferguson, D. M., Jan 24 2008, In : Journal of Medicinal Chemistry. 51, 2, p. 179-182 4 p.

Research output: Contribution to journalArticle

Acridines
Type II DNA Topoisomerase
Pancreatic Neoplasms
Aminacrine
Cell Proliferation
13 Citations (Scopus)

Alternative expressions for energies and forces due to angle bending and torsional energy

Swope, W. C. & Ferguson, D. M., Jun 1992, In : Journal of Computational Chemistry. 13, 5, p. 585-594 10 p.

Research output: Contribution to journalArticle

Molecular mechanics
Torsional stress
Molecular dynamics
Computer program listings
Derivatives
2324 Citations (Scopus)

AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules

Pearlman, D. A., Case, D. A., Caldwell, J. W., Ross, W. S., Cheatham, T. E., DeBolt, S., Ferguson, D., Seibel, G. & Kollman, P., Sep 2 1995, In : Computer Physics Communications. 91, 1-3, p. 1-41 41 p.

Research output: Contribution to journalArticle

Computational chemistry
Molecular mechanics
Free energy
Molecular dynamics
Computer program listings
14 Citations (Scopus)
G-Protein-Coupled Receptors
Proteins
Bacteriorhodopsins
Proline
Mutagenesis
178 Citations (Scopus)

A New Approach to Probing Conformational Space with Molecular Mechanics: Random Incremental Pulse Search

Ferguson, D. M. & Raber, D. J., Jun 1989, In : Journal of the American Chemical Society. 111, 12, p. 4371-4378 8 p.

Research output: Contribution to journalArticle

Molecular mechanics
Mechanics
Cycloparaffins
Potential energy surfaces
Computational methods
14 Citations (Scopus)
Oligodeoxyribonucleotides
Free energy
Decomposition
Organophosphonates
Single-Stranded DNA
81 Citations (Scopus)
Naltrexone
Narcotic Antagonists
Opioid Receptors
Ligands
naltrindole
10340 Citations (Scopus)

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

Bayly, C. I., Merz, K. M., Ferguson, D. M., Cornell, W. D., Fox, T., Caldwell, J. W., Kollman, P. A., Cieplak, P., Gould, I. R. & Spellmeyer, D. C., May 1995, In : Journal of the American Chemical Society. 117, 19, p. 5179-5197 19 p.

Research output: Contribution to journalArticle

Nucleic acids
Static Electricity
Nucleic Acids
Electrostatics
Proteins
34 Citations (Scopus)

A unique binding epitope for salvinorin A, a non-nitrogenous kappa opioid receptor agonist

Kane, B. E., Nieto, M. J., McCurdy, C. R. & Ferguson, D. M., May 1 2006, In : FEBS Journal. 273, 9, p. 1966-1974 9 p.

Research output: Contribution to journalArticle

salvinorin A
kappa Opioid Receptor
Epitopes
Ligands
Opioid Analgesics
6 Citations (Scopus)

Avoiding Antibiotic Inactivation in Mycobacterium tuberculosis by Rv3406 through Strategic Nucleoside Modification

Bockman, M. R., Engelhart, C. A., Dawadi, S., Larson, P., Tiwari, D., Ferguson, D. M., Schnappinger, D. & Aldrich, C. C., Jul 13 2018, In : ACS Infectious Diseases. 4, 7, p. 1102-1113 12 p.

Research output: Contribution to journalArticle

Mycobacterium tuberculosis
Nucleosides
Anti-Bacterial Agents
Ligases
Biotin
91 Citations (Scopus)

Can the Lennard–Jones 6‐12 function replace the 10‐12 form in molecular mechanics calculations?

Ferguson, D. M. & Kollman, P. A., Jun 1991, In : Journal of Computational Chemistry. 12, 5, p. 620-626 7 p.

Research output: Contribution to journalArticle

Molecular Mechanics
Molecular mechanics
Hydrogen Bonds
Hydrogen bonds
Force Field
124 Citations (Scopus)

Cation-π interactions: An energy decomposition analysis and its implication in δ-opioid receptor-ligand binding

Mo, Y., Subramanian, G., Gao, J. & Ferguson, D. M., May 1 2002, In : Journal of the American Chemical Society. 124, 17, p. 4832-4837 6 p.

Research output: Contribution to journalArticle

Opioid Receptors
Cations
Positive ions
Ligands
Decomposition
1 Citation (Scopus)

Combination of Sunitinib and PD-L1 Blockade Enhances Anticancer Efficacy of TLR7/8 Agonist-Based Nanovaccine

Kim, H., Khanna, V., Kucaba, T. A., Zhang, W., Ferguson, D. M., Griffith, T. S. & Panyam, J., Mar 4 2019, In : Molecular Pharmaceutics. 16, 3, p. 1200-1210 11 p.

Research output: Contribution to journalArticle

Cancer Vaccines
Ligands
T-Lymphocytes
Tumor Microenvironment
Nanoparticles
55 Citations (Scopus)

Comparison of ab initio, semiempirical, and molecular mechanics calculations for the conformational analysis of ring systems

Ferguson, D. M., Gould, I. R., Glauser, W. A., Schroeder, S. & Kollman, P. A., May 1992, In : Journal of Computational Chemistry. 13, 4, p. 525-532 8 p.

Research output: Contribution to journalArticle

Molecular Mechanics
Molecular mechanics
Alkanes
Ring
Paraffins
52 Citations (Scopus)

Conformational analysis and automated receptor docking of selective arylacetamide-based κ-opioid agonists

Subramanian, G., Germana Paterlini, M., Larson, D. L., Portoghese, P. S. & Ferguson, D. M., Nov 19 1998, In : Journal of Medicinal Chemistry. 41, 24, p. 4777-4789 13 p.

Research output: Contribution to journalArticle

Opioid Analgesics
Ligands
Molecular Dynamics Simulation
Opiate Alkaloids
Space Flight
79 Citations (Scopus)

Conformational analysis of the endogenous μ-opioid agonist endomorphin-1 using NMR spectroscopy and molecular modeling

Podlogar, B. L., Paterlini, M. G., Ferguson, D. M., Leo, G. C., Demeter, D. A., Brown, F. K. & Reitz, A. B., Nov 13 1998, In : FEBS Letters. 439, 1-2, p. 13-20 8 p.

Research output: Contribution to journalArticle

Molecular modeling
Opioid Analgesics
Nuclear magnetic resonance spectroscopy
Magnetic Resonance Spectroscopy
Ligands
8 Citations (Scopus)

Conformational landscape of selective μ-opioid agonists in gas phase and in aqueous solution: The fentanyl series

Subramanian, G. & Ferguson, D. M., Jul 8 2000, In : Drug Design and Discovery. 17, 1, p. 55-67 13 p.

Research output: Contribution to journalArticle

Fentanyl
Opioid Analgesics
Gases
Quantitative Structure-Activity Relationship
Molecular Dynamics Simulation
7 Citations (Scopus)

Conformational searches for the global minimum of protein models

Ferguson, D. M., Marsh, A., Metzger, T., Garrett, D. G. & Kastella, K., Mar 1 1994, In : Journal of Global Optimization. 4, 2, p. 209-227 19 p.

Research output: Contribution to journalArticle

Global Minimum
Conformation
Conformations
Search Methods
Proteins
119 Citations (Scopus)

Constant temperature simulations using the Langevin equation with velocity Verlet integration

Paterlini, M. G. & Ferguson, D. M., Sep 15 1998, In : Chemical Physics. 236, 1-3, p. 243-252 10 p.

Research output: Contribution to journalArticle

friction
Friction
proteins
Neon
formulations
13 Citations (Scopus)
Open Access
Toll-Like Receptor 8
Toll-Like Receptor 7
Chemical activation
Cytokines
Transcription
86 Citations (Scopus)

Determination of the Relative Binding Free Energies of Peptide Inhibitors to the HIV-1 Protease

Ferguson, D. M., Radmer, R. J. & Kollman, P. A., Aug 1 1991, In : Journal of Medicinal Chemistry. 34, 8, p. 2654-2659 6 p.

Research output: Contribution to journalArticle

18 Citations (Scopus)

Discovery of imidazoquinolines with toll-like receptor 7/8 independent cytokine induction

Shi, C., Xiong, Z., Chittepu, P., Aldrich, C., Ohlfest, J. R. & Ferguson, D. M., May 14 2012, In : ACS Medicinal Chemistry Letters. 3, 6, p. 501-504 4 p.

Research output: Contribution to journalArticle

Toll-Like Receptor 8
Toll-Like Receptor 7
imiquimod
resiquimod
Cytokines
22 Citations (Scopus)

Effects of C2'-Substitution on arabinonucleic acid structure and conformation

Venkateswarlu, D. & Ferguson, D. M., Jun 16 1999, In : Journal of the American Chemical Society. 121, 23, p. 5609-5610 2 p.

Research output: Contribution to journalArticle

Conformations
Substitution reactions
Acids
5 Citations (Scopus)

Efficacy of substituted 9-aminoacridine derivatives in small cell lung cancer

Ryan, E., Jacobson, B. A., Benoit, A., Ferguson, D. M. & Robert, A. K., Apr 1 2013, In : Investigational New Drugs. 31, 2, p. 285-292 8 p.

Research output: Contribution to journalArticle

Aminacrine
Small Cell Lung Carcinoma
Poisons
Cell Proliferation
Psidium
7 Citations (Scopus)

Exploring the unique pharmacology of a novel opioid receptor, ZFOR1, using molecular modeling and the 'message-address' concept

McFadyen, I. J., Metzger, T. G., Paterlini, M. G. & Ferguson, D. M., Dec 1 2001, In : Protein Engineering. 14, 12, p. 953-960 8 p.

Research output: Contribution to journalArticle

Molecular modeling
Opioid Receptors
Ligands
Pharmacology
Opioid Analgesics
27 Citations (Scopus)

Free energy perturbation calculations involving potential function changes

Ferguson, D. M., Pearlman, D. A., Swope, W. C. & Kollman, P. A., Apr 1992, In : Journal of Computational Chemistry. 13, 3, p. 362-370 9 p.

Research output: Contribution to journalArticle

Potential Function
Free energy
Free Energy
Perturbation
Solvation
82 Citations (Scopus)

High-throughput assays using a luciferase-expressing replicon, virus-like particles, and full-length virus for West Nile virus drug discovery

Puig-Basagoiti, F., Deas, T. S., Ren, P., Tilgner, M., Ferguson, D. M. & Shi, P. Y., Dec 1 2005, In : Antimicrobial agents and chemotherapy. 49, 12, p. 4980-4988 9 p.

Research output: Contribution to journalArticle

Flavivirus
West Nile virus
Replicon
Drug Discovery
High-Throughput Screening Assays
31 Citations (Scopus)

How transferable are hydrogen parameters in molecular mechanics calculations?

Veenstra, D. L., Ferguson, D. M. & Kollman, P. A., Oct 1992, In : Journal of Computational Chemistry. 13, 8, p. 971-978 8 p.

Research output: Contribution to journalArticle

Molecular Mechanics
Molecular mechanics
Hydrogen
Van Der Waals
Quantum theory
117 Citations (Scopus)

Identification of compounds with anti-West Nile virus activity

Goodell, J. R., Puig-Basagoiti, F., Forshey, B. M., Shi, P. Y. & Ferguson, D. M., Mar 23 2006, In : Journal of Medicinal Chemistry. 49, 6, p. 2127-2137 11 p.

Research output: Contribution to journalArticle

West Nile virus
West Nile Fever
Quinolines
RNA Helicases
Small Molecule Libraries
1 Citation (Scopus)

Investigation of (S)-(-)-acidomycin: A selective antimycobacterial natural product that inhibits biotin synthase

Bockman, M. R., Engelhart, C. A., Cramer, J. D., Howe, M. D., Mishra, N. K., Zimmerman, M., Larson, P., Alvarez-Cabrera, N., Park, S. W., Boshoff, H. I. M., Bean, J. M., Young, V. G., Ferguson, D. M., Dartois, V., Jarrett, J. T., Schnappinger, D. & Aldrich, C., Apr 12 2019, In : ACS Infectious Diseases. 5, 4, p. 598-617 20 p.

Research output: Contribution to journalArticle

Biological Products
Microbial Sensitivity Tests
Biotin
Tuberculosis
Multidrug-Resistant Tuberculosis
77 Citations (Scopus)
Oxymorphone
Naltrexone
Opioid Receptors
Site-Directed Mutagenesis
naltrindole
28 Citations (Scopus)

Isothermal-isobaric molecular dynamics simulations with Monte Carlo volume sampling

Chow, K. H. & Ferguson, D. M., Sep 2 1995, In : Computer Physics Communications. 91, 1-3, p. 283-289 7 p.

Research output: Contribution to journalArticle

Molecular dynamics
sampling
molecular dynamics
Sampling
Computer simulation
24 Citations (Scopus)

Knowledge-based modeling of a bacterial dichloromethane dehalogenase

Marsh, A. & Ferguson, D. M., Jul 14 1997, In : Proteins: Structure, Function and Genetics. 28, 2, p. 217-226 10 p.

Research output: Contribution to journalArticle

Glutathione Transferase
Methylene Chloride
Catalysis
Methylophilus
Glutathione
77 Citations (Scopus)

Molecular docking reveals a novel binding site model for fentanyl at the μ-opioid receptor

Subramanian, G., Paterlini, M. G., Portoghese, P. S. & Ferguson, D. M., Feb 10 2000, In : Journal of Medicinal Chemistry. 43, 3, p. 381-391 11 p.

Research output: Contribution to journalArticle

Opioid Receptors
Fentanyl
Binding Sites
Ligands
Opiate Alkaloids
28 Citations (Scopus)
Molecular Mechanics
Lanthanoid Series Elements
Molecular mechanics
Coordination Complexes
Metal complexes
38 Citations (Scopus)

Molecular mechanics conformational analysis of cyclononane using the RIPS method and comparison with quantum‐mechanical calculations

Ferguson, D. M., Glauser, W. A. & Raber, D. J., Jan 1 1989, In : Journal of Computational Chemistry. 10, 7, p. 903-910 8 p.

Research output: Contribution to journalArticle

Molecular Mechanics
Molecular mechanics
Conformation
Search Methods
Conformations
67 Citations (Scopus)

Molecular recognition of opioid receptor ligands

Kane, B. E., Svensson, B. & Ferguson, D. M., Mar 10 2006, In : AAPS Journal. 8, 1, 15.

Research output: Contribution to journalArticle

Opioid Receptors
Ligands
Opiate Alkaloids
Recombinant DNA
Site-Directed Mutagenesis
72 Citations (Scopus)
Dynorphins
Chemical activation
Opioid Analgesics
Opioid Receptors
Ligands
17 Citations (Scopus)

New Results on Protein Folding from Simulated Annealing

Garrett, D. G., Kastella, K. & Ferguson, D. M., Jul 1 1992, In : Journal of the American Chemical Society. 114, 16, p. 6555-6556 2 p.

Research output: Contribution to journalArticle

Protein folding
Protein Folding
Simulated annealing
11 Citations (Scopus)
Topoisomerase II Inhibitors
Acridines
Mesothelioma
Cell Proliferation
Apoptosis
59 Citations (Scopus)

Novel acridine-based compounds that exhibit an anti-pancreatic cancer activity are catalytic inhibitors of human topoisomerase II

Oppegard, L. M., Ougolkov, A. V., Luchini, D. N., Schoon, R. A., Goodell, J. R., Kaur, H., Billadeau, D. D., Ferguson, D. M. & Hiasa, H., Jan 14 2009, In : European Journal of Pharmacology. 602, 2-3, p. 223-229 7 p.

Research output: Contribution to journalArticle

Topoisomerase II Inhibitors
Acridines
Type II DNA Topoisomerase
Pancreatic Neoplasms
Amsacrine
70 Citations (Scopus)

On the role of extracellular loops of opioid receptors in conferring ligand selectivity

Metzger, T. G. & Ferguson, D. M., Nov 13 1995, In : FEBS Letters. 375, 1-2, p. 1-4 4 p.

Research output: Contribution to journalArticle

Opioid Receptors
Opioid Analgesics
Ligands
Mutagenesis
Site-Directed Mutagenesis
14 Citations (Scopus)

On the role of topoisomerase I in mediating the cytotoxicity of 9-aminoacridine-based anticancer agents

Gálvez-Peralta, M., Hackbarth, J. S., Flatten, K. S., Kaufmann, S. H., Hiasa, H., Xing, C. & Ferguson, D. M., Aug 1 2009, In : Bioorganic and Medicinal Chemistry Letters. 19, 15, p. 4459-4462 4 p.

Research output: Contribution to journalArticle

Aminacrine
Type I DNA Topoisomerase
Cytotoxicity
Antineoplastic Agents
Cells
115 Citations (Scopus)

Parameterization and evaluation of a flexible water model

Ferguson, D. M., Apr 1995, In : Journal of Computational Chemistry. 16, 4, p. 501-511 11 p.

Research output: Contribution to journalArticle

Parameterization
Water
Evaluation
Water Potential
Dielectric Properties