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Items: 1 to 50 of 200

1.

Absolute Free Energy of Binding Calculations for Macrophage Migration Inhibitory Factor in Complex with a Druglike Inhibitor.

Qian Y, Cabeza de Vaca I, Vilseck JZ, Cole DJ, Tirado-Rives J, Jorgensen WL.

J Phys Chem B. 2019 Oct 17;123(41):8675-8685. doi: 10.1021/acs.jpcb.9b07588. Epub 2019 Oct 7.

PMID:
31553604
2.

Structure activity relationship towards design of cryptosporidium specific thymidylate synthase inhibitors.

Czyzyk DJ, Valhondo M, Deiana L, Tirado-Rives J, Jorgensen WL, Anderson KS.

Eur J Med Chem. 2019 Dec 1;183:111673. doi: 10.1016/j.ejmech.2019.111673. Epub 2019 Sep 4.

PMID:
31536894
3.

Computation of protein-ligand binding free energies using quantum mechanical bespoke force fields.

Cole DJ, Cabeza de Vaca I, Jorgensen WL.

Medchemcomm. 2019 Feb 27;10(7):1116-1120. doi: 10.1039/c9md00017h. eCollection 2019 Jul 1.

PMID:
31391883
4.

Molecular and cellular studies evaluating a potent 2-cyanoindolizine catechol diether NNRTI targeting wildtype and Y181C mutant HIV-1 reverse transcriptase.

Sasaki T, Gannam ZTK, Kudalkar SN, Frey KM, Lee WG, Spasov KA, Jorgensen WL, Anderson KS.

Bioorg Med Chem Lett. 2019 Aug 15;29(16):2182-2188. doi: 10.1016/j.bmcl.2019.06.047. Epub 2019 Jun 26.

PMID:
31281023
5.

QM/MM Calculations for the Cl- + CH3Cl SN2 Reaction in Water Using CM5 Charges and Density Functional Theory.

Tirado-Rives J, Jorgensen WL.

J Phys Chem A. 2019 Jul 11;123(27):5713-5717. doi: 10.1021/acs.jpca.9b04121. Epub 2019 Jun 27.

PMID:
31246023
6.

Robust Free Energy Perturbation Protocols for Creating Molecules in Solution.

Cabeza de Vaca I, Zarzuela R, Tirado-Rives J, Jorgensen WL.

J Chem Theory Comput. 2019 Jul 9;15(7):3941-3948. doi: 10.1021/acs.jctc.9b00213. Epub 2019 Jun 24.

PMID:
31185169
7.

Understanding the structural basis of species selective, stereospecific inhibition for Cryptosporidium and human thymidylate synthase.

Czyzyk DJ, Valhondo M, Jorgensen WL, Anderson KS.

FEBS Lett. 2019 Aug;593(15):2069-2078. doi: 10.1002/1873-3468.13474. Epub 2019 Jun 18.

PMID:
31172516
8.

Structural and pharmacological evaluation of a novel non-nucleoside reverse transcriptase inhibitor as a promising long acting nanoformulation for treating HIV.

Kudalkar SN, Ullah I, Bertoletti N, Mandl HK, Cisneros JA, Beloor J, Chan AH, Quijano E, Saltzman WM, Jorgensen WL, Kumar P, Anderson KS.

Antiviral Res. 2019 Jul;167:110-116. doi: 10.1016/j.antiviral.2019.04.010. Epub 2019 Apr 26.

PMID:
31034849
9.

Novel allosteric covalent inhibitors of bifunctional Cryptosporidium hominis TS-DHFR from parasitic protozoa identified by virtual screening.

Ruiz V, Czyzyk DJ, Valhondo M, Jorgensen WL, Anderson KS.

Bioorg Med Chem Lett. 2019 Jun 1;29(11):1413-1418. doi: 10.1016/j.bmcl.2019.03.022. Epub 2019 Mar 20.

PMID:
30929953
10.

Development and Testing of the OPLS-AA/M Force Field for RNA.

Robertson MJ, Qian Y, Robinson MC, Tirado-Rives J, Jorgensen WL.

J Chem Theory Comput. 2019 Apr 9;15(4):2734-2742. doi: 10.1021/acs.jctc.9b00054. Epub 2019 Mar 12.

PMID:
30807148
11.

Molecular Dynamics Simulations of a Conformationally Mobile Peptide-Based Catalyst for Atroposelective Bromination.

Yan XC, Metrano AJ, Robertson MJ, Abascal NC, Tirado-Rives J, Miller SJ, Jorgensen WL.

ACS Catal. 2018 Nov 2;8(11):9968-9979. doi: 10.1021/acscatal.8b03563. Epub 2018 Sep 13.

12.

Unbinding Dynamics of Non-Nucleoside Inhibitors from HIV-1 Reverse Transcriptase.

Dodda LS, Tirado-Rives J, Jorgensen WL.

J Phys Chem B. 2019 Feb 28;123(8):1741-1748. doi: 10.1021/acs.jpcb.8b10341. Epub 2019 Jan 3.

PMID:
30571126
13.

Reply to Pandey et al.: Understanding the efficacy of a potential antiretroviral drug candidate in humanized mouse model of HIV infection.

Kudalkar SN, Beloor J, Quijano E, Spasov KA, Lee WG, Cisneros JA, Saltzman WM, Kumar P, Jorgensen WL, Anderson KS.

Proc Natl Acad Sci U S A. 2018 Aug 28;115(35):E8114-E8115. doi: 10.1073/pnas.1810136115. Epub 2018 Aug 10. No abstract available.

14.

Advances and Insights for Small Molecule Inhibition of Macrophage Migration Inhibitory Factor.

Trivedi-Parmar V, Jorgensen WL.

J Med Chem. 2018 Sep 27;61(18):8104-8119. doi: 10.1021/acs.jmedchem.8b00589. Epub 2018 Jun 4.

15.

Enhanced Monte Carlo Methods for Modeling Proteins Including Computation of Absolute Free Energies of Binding.

Cabeza de Vaca I, Qian Y, Vilseck JZ, Tirado-Rives J, Jorgensen WL.

J Chem Theory Comput. 2018 Jun 12;14(6):3279-3288. doi: 10.1021/acs.jctc.8b00031. Epub 2018 May 8.

16.

Optimization of Pyrazoles as Phenol Surrogates to Yield Potent Inhibitors of Macrophage Migration Inhibitory Factor.

Trivedi-Parmar V, Robertson MJ, Cisneros JA, Krimmer SG, Jorgensen WL.

ChemMedChem. 2018 Jun 6;13(11):1092-1097. doi: 10.1002/cmdc.201800158. Epub 2018 Apr 23.

17.

Improved Treatment of Nucleosides and Nucleotides in the OPLS-AA Force Field.

Robertson MJ, Tirado-Rives J, Jorgensen WL.

Chem Phys Lett. 2017 Sep 1;683:276-280. doi: 10.1016/j.cplett.2017.02.049. Epub 2017 Feb 16.

18.

From in silico hit to long-acting late-stage preclinical candidate to combat HIV-1 infection.

Kudalkar SN, Beloor J, Quijano E, Spasov KA, Lee WG, Cisneros JA, Saltzman WM, Kumar P, Jorgensen WL, Anderson KS.

Proc Natl Acad Sci U S A. 2018 Jan 23;115(4):E802-E811. doi: 10.1073/pnas.1717932115. Epub 2017 Dec 26. Erratum in: Proc Natl Acad Sci U S A. 2018 Mar 12;:.

19.

Adding a Hydrogen Bond May Not Help: Naphthyridinone vs Quinoline Inhibitors of Macrophage Migration Inhibitory Factor.

Dawson TK, Dziedzic P, Robertson MJ, Cisneros JA, Krimmer SG, Newton AS, Tirado-Rives J, Jorgensen WL.

ACS Med Chem Lett. 2017 Nov 14;8(12):1287-1291. doi: 10.1021/acsmedchemlett.7b00384. eCollection 2017 Dec 14.

20.

Covalent inhibitors for eradication of drug-resistant HIV-1 reverse transcriptase: From design to protein crystallography.

Chan AH, Lee WG, Spasov KA, Cisneros JA, Kudalkar SN, Petrova ZO, Buckingham AB, Anderson KS, Jorgensen WL.

Proc Natl Acad Sci U S A. 2017 Sep 5;114(36):9725-9730. doi: 10.1073/pnas.1711463114. Epub 2017 Aug 21.

21.

Computationally-guided optimization of small-molecule inhibitors of the Aurora A kinase-TPX2 protein-protein interaction.

Cole DJ, Janecek M, Stokes JE, Rossmann M, Faver JC, McKenzie GJ, Venkitaraman AR, Hyvönen M, Spring DR, Huggins DJ, Jorgensen WL.

Chem Commun (Camb). 2017 Aug 17;53(67):9372-9375. doi: 10.1039/c7cc05379g.

22.

Improved Description of Sulfur Charge Anisotropy in OPLS Force Fields: Model Development and Parameterization.

Yan XC, Robertson MJ, Tirado-Rives J, Jorgensen WL.

J Phys Chem B. 2017 Jul 13;121(27):6626-6636. doi: 10.1021/acs.jpcb.7b04233. Epub 2017 Jun 29.

23.

Identification and Characterization of JAK2 Pseudokinase Domain Small Molecule Binders.

Puleo DE, Kucera K, Hammarén HM, Ungureanu D, Newton AS, Silvennoinen O, Jorgensen WL, Schlessinger J.

ACS Med Chem Lett. 2017 May 17;8(6):618-621. doi: 10.1021/acsmedchemlett.7b00153. eCollection 2017 Jun 8.

24.

JAK2 JH2 Fluorescence Polarization Assay and Crystal Structures for Complexes with Three Small Molecules.

Newton AS, Deiana L, Puleo DE, Cisneros JA, Cutrona KJ, Schlessinger J, Jorgensen WL.

ACS Med Chem Lett. 2017 May 17;8(6):614-617. doi: 10.1021/acsmedchemlett.7b00154. eCollection 2017 Jun 8.

25.

LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands.

Dodda LS, Cabeza de Vaca I, Tirado-Rives J, Jorgensen WL.

Nucleic Acids Res. 2017 Jul 3;45(W1):W331-W336. doi: 10.1093/nar/gkx312.

26.

1.14*CM1A-LBCC: Localized Bond-Charge Corrected CM1A Charges for Condensed-Phase Simulations.

Dodda LS, Vilseck JZ, Tirado-Rives J, Jorgensen WL.

J Phys Chem B. 2017 Apr 20;121(15):3864-3870. doi: 10.1021/acs.jpcb.7b00272. Epub 2017 Mar 2.

27.

Structural and Preclinical Studies of Computationally Designed Non-Nucleoside Reverse Transcriptase Inhibitors for Treating HIV infection.

Kudalkar SN, Beloor J, Chan AH, Lee WG, Jorgensen WL, Kumar P, Anderson KS.

Mol Pharmacol. 2017 Apr;91(4):383-391. doi: 10.1124/mol.116.107755. Epub 2017 Feb 6.

28.

Systematic Study of Effects of Structural Modifications on the Aqueous Solubility of Drug-like Molecules.

Cisneros JA, Robertson MJ, Mercado BQ, Jorgensen WL.

ACS Med Chem Lett. 2016 Dec 1;8(1):124-127. doi: 10.1021/acsmedchemlett.6b00451. eCollection 2017 Jan 12.

29.

Design, Conformation, and Crystallography of 2-Naphthyl Phenyl Ethers as Potent Anti-HIV Agents.

Lee WG, Chan AH, Spasov KA, Anderson KS, Jorgensen WL.

ACS Med Chem Lett. 2016 Oct 31;7(12):1156-1160. eCollection 2016 Dec 8.

30.

Computer-aided discovery of anti-HIV agents.

Jorgensen WL.

Bioorg Med Chem. 2016 Oct 15;24(20):4768-4778. doi: 10.1016/j.bmc.2016.07.039. Epub 2016 Jul 21.

31.

Performance of Protein-Ligand Force Fields for the Flavodoxin-Flavin Mononucleotide System.

Robertson MJ, Tirado-Rives J, Jorgensen WL.

J Phys Chem Lett. 2016 Aug 4;7(15):3032-6. doi: 10.1021/acs.jpclett.6b01229. Epub 2016 Jul 26.

32.

A Fluorescence Polarization Assay for Binding to Macrophage Migration Inhibitory Factor and Crystal Structures for Complexes of Two Potent Inhibitors.

Cisneros JA, Robertson MJ, Valhondo M, Jorgensen WL.

J Am Chem Soc. 2016 Jul 13;138(27):8630-8. doi: 10.1021/jacs.6b04910. Epub 2016 Jun 28.

33.

Irregularities in enzyme assays: The case of macrophage migration inhibitory factor.

Cisneros JA, Robertson MJ, Valhondo M, Jorgensen WL.

Bioorg Med Chem Lett. 2016 Jun 15;26(12):2764-2767. doi: 10.1016/j.bmcl.2016.04.074. Epub 2016 Apr 26.

PMID:
27156768
34.

Biomolecular Force Field Parameterization via Atoms-in-Molecule Electron Density Partitioning.

Cole DJ, Vilseck JZ, Tirado-Rives J, Payne MC, Jorgensen WL.

J Chem Theory Comput. 2016 May 10;12(5):2312-23. doi: 10.1021/acs.jctc.6b00027. Epub 2016 Apr 21.

35.

Hydration Properties and Solvent Effects for All-Atom Solutes in Polarizable Coarse-Grained Water.

Yan XC, Tirado-Rives J, Jorgensen WL.

J Phys Chem B. 2016 Aug 25;120(33):8102-14. doi: 10.1021/acs.jpcb.6b00399. Epub 2016 Mar 1.

36.

OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins.

Harder E, Damm W, Maple J, Wu C, Reboul M, Xiang JY, Wang L, Lupyan D, Dahlgren MK, Knight JL, Kaus JW, Cerutti DS, Krilov G, Jorgensen WL, Abel R, Friesner RA.

J Chem Theory Comput. 2016 Jan 12;12(1):281-96. doi: 10.1021/acs.jctc.5b00864. Epub 2015 Dec 1.

PMID:
26584231
37.

Evaluation of CM5 Charges for Nonaqueous Condensed-Phase Modeling.

Dodda LS, Vilseck JZ, Cutrona KJ, Jorgensen WL.

J Chem Theory Comput. 2015 Sep 8;11(9):4273-82. doi: 10.1021/acs.jctc.5b00414. Epub 2015 Aug 27.

38.

A reflection on Paul von Ragué Schleyer.

Jorgensen WL.

J Chem Theory Comput. 2015 Jan 13;11(1):1. doi: 10.1021/ct501095w. No abstract available.

PMID:
26574196
39.

Potent Inhibitors Active against HIV Reverse Transcriptase with K101P, a Mutation Conferring Rilpivirine Resistance.

Gray WT, Frey KM, Laskey SB, Mislak AC, Spasov KA, Lee WG, Bollini M, Siliciano RF, Jorgensen WL, Anderson KS.

ACS Med Chem Lett. 2015 Aug 31;6(10):1075-9. doi: 10.1021/acsmedchemlett.5b00254. eCollection 2015 Oct 8.

40.

Application of a BOSS-Gaussian interface for QM/MM simulations of Henry and methyl transfer reactions.

Vilseck JZ, Kostal J, Tirado-Rives J, Jorgensen WL.

J Comput Chem. 2015 Oct 15;36(27):2064-74. doi: 10.1002/jcc.24045. Epub 2015 Aug 27.

41.

Improved Peptide and Protein Torsional Energetics with the OPLSAA Force Field.

Robertson MJ, Tirado-Rives J, Jorgensen WL.

J Chem Theory Comput. 2015 Jul 14;11(7):3499-509.

42.

Discovery and crystallography of bicyclic arylaminoazines as potent inhibitors of HIV-1 reverse transcriptase.

Lee WG, Frey KM, Gallardo-Macias R, Spasov KA, Chan AH, Anderson KS, Jorgensen WL.

Bioorg Med Chem Lett. 2015 Nov 1;25(21):4824-4827. doi: 10.1016/j.bmcl.2015.06.074. Epub 2015 Jul 9.

43.

Macrophage Migration Inhibitory Factor Is Detrimental in Pneumococcal Pneumonia and a Target for Therapeutic Immunomodulation.

Weiser JN, Roche AM, Hergott CB, LaRose MI, Connolly T, Jorgensen WL, Leng L, Bucala R, Das R.

J Infect Dis. 2015 Nov 15;212(10):1677-82. doi: 10.1093/infdis/jiv262. Epub 2015 May 5.

44.

A nanotherapy strategy significantly enhances anticryptosporidial activity of an inhibitor of bifunctional thymidylate synthase-dihydrofolate reductase from Cryptosporidium.

Mukerjee A, Iyidogan P, Castellanos-Gonzalez A, Cisneros JA, Czyzyk D, Ranjan AP, Jorgensen WL, White AC Jr, Vishwanatha JK, Anderson KS.

Bioorg Med Chem Lett. 2015;25(10):2065-7. doi: 10.1016/j.bmcl.2015.03.091. Epub 2015 Apr 4.

45.

Structure-based evaluation of non-nucleoside inhibitors with improved potency and solubility that target HIV reverse transcriptase variants.

Frey KM, Puleo DE, Spasov KA, Bollini M, Jorgensen WL, Anderson KS.

J Med Chem. 2015 Mar 26;58(6):2737-45. doi: 10.1021/jm501908a. Epub 2015 Mar 5.

46.

Design, synthesis, and protein crystallography of biaryltriazoles as potent tautomerase inhibitors of macrophage migration inhibitory factor.

Dziedzic P, Cisneros JA, Robertson MJ, Hare AA, Danford NE, Baxter RH, Jorgensen WL.

J Am Chem Soc. 2015 Mar 4;137(8):2996-3003. doi: 10.1021/ja512112j. Epub 2015 Feb 20.

47.

Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field.

Wang L, Wu Y, Deng Y, Kim B, Pierce L, Krilov G, Lupyan D, Robinson S, Dahlgren MK, Greenwood J, Romero DL, Masse C, Knight JL, Steinbrecher T, Beuming T, Damm W, Harder E, Sherman W, Brewer M, Wester R, Murcko M, Frye L, Farid R, Lin T, Mobley DL, Jorgensen WL, Berne BJ, Friesner RA, Abel R.

J Am Chem Soc. 2015 Feb 25;137(7):2695-703. doi: 10.1021/ja512751q. Epub 2015 Feb 12.

PMID:
25625324
48.

Endothelial CD74 mediates macrophage migration inhibitory factor protection in hyperoxic lung injury.

Sauler M, Zhang Y, Min JN, Leng L, Shan P, Roberts S, Jorgensen WL, Bucala R, Lee PJ.

FASEB J. 2015 May;29(5):1940-9. doi: 10.1096/fj.14-260299. Epub 2015 Jan 21.

49.

Autobiography of William L. Jorgensen: scientific history and recollections.

Jorgensen WL.

J Phys Chem B. 2015 Jan 22;119(3):624-32. doi: 10.1021/jp510442j. No abstract available.

PMID:
25608799
50.

Determination of partial molar volumes from free energy perturbation theory.

Vilseck JZ, Tirado-Rives J, Jorgensen WL.

Phys Chem Chem Phys. 2015 Apr 7;17(13):8407-15. doi: 10.1039/c4cp05304d. Epub 2015 Jan 15.

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