Publications

2025 The need to implement FAIR principles in biomolecular simulations William Jorgensen · Nature Methods · Scholar only 91 2021 A Reflection on Norman Louis Allinger. William Jorgensen · Journal of Chemical Theory and Computation 1 2021 Covalent Inhibition of Wild-Type HIV-1 Reverse Transcriptase Using a Fluorosulfate Warhead. William Jorgensen · ACS Medicinal Chemistry Letters 28 2021 Indoloxytriazenes as binding molecules for the JAK2 JH2 pseudokinase domain and its V617F variant. William Jorgensen · Tetrahedron Letters 13 2021 Long-acting and extended-release implant and nanoformulations with a synergistic antiretroviral two-drug combination controls HIV-1 infection in a humanized mouse model. William Jorgensen · Bioengineering & Translational Medicine 13 2021 Optimization of Triarylpyridinone Inhibitors of the Main Protease of SARS-CoV-2 to Low-Nanomolar Antiviral Potency. William Jorgensen · ACS Medicinal Chemistry Letters 58 2021 Potent non-covalent inhibitors of the main protease of SARS-CoV-2 from molecular sculpting of the drug parampanel guided by free-energy perturbation calculations. William Jorgensen · ACS Central Science 300 2021 Pyrazole-Containing Macrophage Migration Inhibitory Factor Inhibitors William Jorgensen · US Patent App. 16/979,306 — 2021 Structural insights into a novel perampanel-derived pharmacophore targeting the SARS- CoV-2 main protease. William Jorgensen · Structure 63 2020 Explicit Representation of Cation-π Interactions in Force Fields with 1/r4 Non-bonded Terms. William Jorgensen · Journal of Chemical Theory and Computation 38 2020 Identification of 14 Known Drugs as Inhibitors of the Main Protease of SARS-CoV-2. William Jorgensen · ACS Medicinal Chemistry Letters 244 2020 Metadynamics as a Post-Processing Method for Virtual Screening with Application to the Pseudokinase Domain of JAK2. William Jorgensen · Journal of Chemical Information and Modeling 27 2020 Selective JAK2 Pseudokinase Ligands with a Diaminotriazole Core. William Jorgensen · Journal of Medicinal Chemistry 26 2020 Structural Investigation of 2-Naphthyl Phenyl Ether Inhibitors Bound to WT and Y181C Reverse Transcriptase Highlights Key Features of the NNRTI Binding Site. William Jorgensen · Protein Science 12 2020 Structure-Guided Identification of DNMT3B Inhibitors. William Jorgensen · ACS Medicinal Chemistry Letters 20 2020 Targeting the TS dimer interface in bifunctional Cryptosporidium hominis TS-DHFR from parasitic protozoa: Virtual screening identifies novel TS allosteric inhibitors. William Jorgensen · Bioorganic & Medicinal Chemistry Letters 3 2019 Absolute Free Energy of Binding Calculations for Macrophage Migration Inhibitory Factor in Complex with a Drug-like Inhibitor. William Jorgensen · The Journal of Physical Chemistry B 31 2019 Computation of Protein-Ligand Binding Free Energies Using Quantum Mechanical Bespoke Force Fields. William Jorgensen · MedChemComm 31 2019 Development and Testing of the OPLS-AA/M Force Field for RNA. William Jorgensen · Journal of Chemical Theory and Computation 124 2019 Macrophage Migration Inhibitory Factor Inhibitors, and Methods of Making and Using Same William Jorgensen · US Patent Publ. No. 20190144424 — 2019 Molecular and Cellular Studies Evaluating a Potent 2-Cyanoindolizine Catechol Diether NNRTI Targeting Wildtype and Y181C Mutant HIV-1 Reverse Transcriptase William Jorgensen · Bioorganic & Medicinal Chemistry Letters 7 2019 New 7,8-Dihydro-1,7-naphthyridin-8-one compounds used for treating an inflammatory disease, autoimmune disease and cancer, and disease associated with high macrophage migration inhibitory factor expression William Jorgensen · US2019144424-A1 — 2019 New substituted 4-phenyl-1H-pyrazole compounds are macrophage migration inhibitory factor inhibitors, useful for treating an inflammatory disease, a neurological disorder, and/or cancer William Jorgensen · WO2019178480-A1 — 2019 Novel Allosteric Covalent Inhibitors of Bifunctional Cryptosporidium hominis TS- DHFR from Parasitic Protozoa Identified by Virtual Screening. William Jorgensen · Bioorganic & Medicinal Chemistry Letters 9 2019 QM/MM Calculations for the Cl- + CH3Cl SN2 Reaction in Water Using CM5 Charges and Density Functional Theory. William Jorgensen · The Journal of Physical Chemistry A 18 2019 Robust FEP Protocols for Creating Molecules in Solution. William Jorgensen · Journal of Chemical Theory and Computation 28 2019 Structural and Pharmacological Evaluation of a Novel Non-nucleoside Reverse Transcriptase Inhibitor as a Promising Long Acting Nanoformulation for Treating HIV. William Jorgensen · Antiviral Research 27 2019 Structure Activity Relationship Towards the Design of Cryptosporidium Specific Thymidylate Synthase Inhibitors. William Jorgensen · European Journal of Medicinal Chemistry 7 2019 Unbinding Dynamics of Non-Nucleoside Inhibitors from HIV-1 Reverse Transcriptase. William Jorgensen · The Journal of Physical Chemistry B 27 2019 Understanding the Structural Basis of Species Selective, Stereospecific Inhibition for Cryptosporidium and Human Thymidylate Synthase. William Jorgensen · FEBS Letters 5 2018 Advances and Insights for Small Molecule Inhibition of Macrophage Migration Inhibitory Factor. William Jorgensen · Journal of Medicinal Chemistry 51 2018 Biaryltriazole inhibitors of macrophage migration inhibitory factor William Jorgensen · US Patent Publ. No. 20180179176 — 2018 Enhanced Monte Carlo Methods for Modeling Proteins Including Computation of Absolute Free Energies of Binding. William Jorgensen · Journal of Chemical Theory and Computation 49 2018 From In Silico Hit to Long-Acting Late-Stage Preclinical Candidate to Combat HIV Infection. William Jorgensen · Proceedings of the National Academy of Sciences 36 2018 Molecular Dynamics Simulations of a Conformationally Mobile Peptide-Based Catalyst for Atroposelective Bromination. William Jorgensen · ACS Catalysis 33 2018 Optimization of Pyrazoles as Phenol Surrogates to Yield Potent Inhibitors of Macrophage Migration Inhibitory Factor. William Jorgensen · ChemMedChem 20 2017 Adding a Hydrogen Bond May Not Help: Naphthyridinone vs. Quinoline Inhibitors of Macrophage Migration Inhibitory Factor. William Jorgensen · ACS Medicinal Chemistry Letters 11 2017 Computationally-Guided Optimization of Small-Molecule Inhibitors of the Aurora A Kinase – TPX2 Protein-Protein Interaction. William Jorgensen · Chemical Communications 17 2017 Covalent inhibitors for eradication of drug-resistant HIV-1 reverse transcriptase: from design to protein crystallography. William Jorgensen · Proceedings of the National Academy of Sciences 51 2017 Identification and Characterization of Small Molecules Binding to the JAK2 Pseudokinase Domain. William Jorgensen · ACS Medicinal Chemistry Letters 49 2017 Improved Description of Sulfur Anisotropy in OPLS Force Fields. Model Development and Parameterization. William Jorgensen · The Journal of Physical Chemistry B 49 2017 Improved Treatment of Nucleosides and Nucleotides in the OPLS-AA Force Field. William Jorgensen · Chemical Physics Letters 25 2017 JAK2-JH2 Fluorescence Polarization Assay and Crystal Structures for Complexes with Three Small Molecules. William Jorgensen · ACS Medicinal Chemistry Letters 30 2017 LigParGen web server: An automatic OPLS-AA parameter generator for organic molecules. William Jorgensen · Nucleic Acids Research 2,056 2017 Localized Bond Charge Corrected CM1A Charges for Condensed-Phase Simulations. William Jorgensen · The Journal of Physical Chemistry B 1,010 2017 MIF modulators William Jorgensen · US Patent 9,540,322 — 2017 Structural and Preclinical Studies of Computationally-Designed Non-nucleoside Reverse Transcriptase Inhibitors for Treating HIV Infection. William Jorgensen · Molecular Pharmacology 19 2017 Systematic Study of Effects of Structural Modifications on the Aqueous Solubilities of Drug-like Molecules. William Jorgensen · ACS Medicinal Chemistry Letters 43 2016 A Fluorescence Polarization Assay for Binding to Macrophage Migration Inhibitory Factor and Crystal Structures for Two Potent Complexes William Jorgensen · Journal of the American Chemical Society 46 2016 Biomolecular Force Field Parameterization via Atoms-in-Molecule Electron Density Partitioning William Jorgensen · Journal of Chemical Theory and Computation 182