Fragment-based design of small molecule PCSK9 inhibitors using simulated annealing of chemical potential simulations

Autoři: Frank Guarnieri aff001;  John L. Kulp, Jr. aff003;  John L. Kulp, III aff003;  Ian S. Cloudsdale aff003
Působiště autorů: Center for Drug Discovery, Northeastern University, Boston, MA, United States of America aff001;  PAKA Pulmonary Pharmaceuticals, Acton, MA, United States of America aff002;  Conifer Point Pharmaceuticals, Doylestown, PA, United States of America aff003;  Department of Chemistry, Baruch S. Blumberg Institute, Doylestown, PA, United States of America aff004
Vyšlo v časopise: PLoS ONE 14(12)
Kategorie: Research Article


PCSK9 is a protein secreted by the liver that binds to the low-density lipoprotein receptor (LDLR), causing LDLR internalization, decreasing the clearance of circulating LDL particles. Mutations in PCSK9 that strengthen its interactions with LDLR result in familial hypercholesterolemia (FH) and early onset atherosclerosis, while nonsense mutations of PCSK9 result in cardio-protective hypocholesterolemia. These observations led to PCSK9 inhibition for cholesterol lowering becoming a high-interest therapeutic target, with antibody drugs reaching the market. An orally-available small molecule drug is highly desirable, but inhibiting the PCSK9/LDLR protein-protein interaction (PPI) has proven challenging. Alternate approaches to finding good lead candidates are needed. Motivated by the FH mutation data on PCSK9, we found that modeling the PCSK9/LDLR interface revealed extensive electron delocalization between and within the protein partners. Based on this, we hypothesized that compounds assembled from chemical fragments could achieve the affinity required to inhibit the PCSK9/LDLR PPI if they were selected to interact with PCSK9 in a way that, like LDLR, also involves significant fractional charge transfer to form partially covalent bonds. To identify such fragments, Simulated Annealing of Chemical Potential (SACP) fragment simulations were run on multiple PCSK9 structures, using optimized partial charges for the protein. We designed a small molecule, composed of several fragments, predicted to interact at two sites on the PCSK9. This compound inhibits the PPI with 1 μM affinity. Further, we designed two similar small molecules where one allows charge delocalization though a linker and the other doesn’t. The first inhibitor with charge delocalization enhances LDLR surface expression by 60% at 10 nM, two orders of magnitude more potent than the EGF domain of LDLR. The other enhances LDLR expression by only 50% at 1 μM. This supports our conjecture that fragments can have surprisingly outsized efficacy in breaking PPI’s by achieving fractional charge transfer leading to partially covalent bonding.

Klíčová slova:

Biochemical simulations – Carbon – Drug discovery – Hydrogen bonding – Protein interactions – Salt bridges – Small molecules


1. Goldstein JL, Brown MS. Familial hypercholesterolemia: pathogenesis of a receptor disease. Johns Hopkins Med J. 1978;143(1):8–16. Epub 1978/07/01. 209238.

2. Innerarity TL, Weisgraber KH, Arnold KS, Mahley RW, Krauss RM, Vega GL, et al. Familial defective apolipoprotein B-100: low density lipoproteins with abnormal receptor binding. Proc Natl Acad Sci U S A. 1987;84(19):6919–23. Epub 1987/10/01. doi: 10.1073/pnas.84.19.6919 3477815; PubMed Central PMCID: PMC299196.

3. Abifadel M, Elbitar S, El Khoury P, Ghaleb Y, Chemaly M, Moussalli ML, et al. Living the PCSK9 adventure: from the identification of a new gene in familial hypercholesterolemia towards a potential new class of anticholesterol drugs. Curr Atheroscler Rep. 2014;16(9):439. Epub 2014/07/24. doi: 10.1007/s11883-014-0439-8 25052769

4. Ajufo E, Rader DJ. Recent advances in the pharmacological management of hypercholesterolaemia. Lancet Diabetes Endocrinol. 2016;4(5):436–46. Epub 2016/03/26. doi: 10.1016/S2213-8587(16)00074-7 [pii]. 27012540.

5. Bauer RC, Khetarpal SA, Hand NJ, Rader DJ. Therapeutic Targets of Triglyceride Metabolism as Informed by Human Genetics. Trends Mol Med. 2016;22(4):328–40. Epub 2016/03/19. doi: 10.1016/j.molmed.2016.02.005 [pii]. 26988439.

6. Besseling J, Sjouke B, Kastelein JJ. Screening and treatment of familial hypercholesterolemia—Lessons from the past and opportunities for the future (based on the Anitschkow Lecture 2014). Atherosclerosis. 2015;241(2):597–606. Epub 2015/06/27. doi: 10.1016/j.atherosclerosis.2015.06.011 [pii]. 26115072.

7. Brautbar A, Leary E, Rasmussen K, Wilson DP, Steiner RD, Virani S. Genetics of familial hypercholesterolemia. Curr Atheroscler Rep. 2015;17(4):491. Epub 2015/02/26. doi: 10.1007/s11883-015-0491-z 25712136.

8. Bruikman CS, Hovingh GK, Kastelein JJ. Molecular basis of familial hypercholesterolemia. Curr Opin Cardiol. 2017. Epub 2017/02/09. doi: 10.1097/HCO.0000000000000385 28169949.

9. Di Taranto MD, D'Agostino MN, Fortunato G. Functional characterization of mutant genes associated with autosomal dominant familial hypercholesterolemia: integration and evolution of genetic diagnosis. Nutr Metab Cardiovasc Dis. 2015;25(11):979–87. Epub 2015/07/15. doi: 10.1016/j.numecd.2015.06.007 [pii]. 26165249.

10. Dron JS, Hegele RA. Complexity of mechanisms among human proprotein convertase subtilisin-kexin type 9 variants. Curr Opin Lipidol. 2017. Epub 2017/02/06. doi: 10.1097/MOL.0000000000000386 28157721.

11. Gabcova-Balaziova D, Stanikova D, Vohnout B, Huckova M, Stanik J, Klimes I, et al. Molecular-genetic aspects of familial hypercholesterolemia. Endocr Regul. 2015;49(3):164–81. Epub 2015/08/05. doi: 10.4149/endo_2015_03_164 26238499.

12. Hartgers ML, Ray KK, Hovingh GK. New Approaches in Detection and Treatment of Familial Hypercholesterolemia. Curr Cardiol Rep. 2015;17(12):109. Epub 2015/10/21. doi: 10.1007/s11886-015-0665-x [pii]. 26482752; PubMed Central PMCID: PMC4611021.

13. Henderson R, O'Kane M, McGilligan V, Watterson S. The genetics and screening of familial hypercholesterolaemia. J Biomed Sci. 2016;23:39. Epub 2016/04/17. doi: 10.1186/s12929-016-0256-1 [pii]. 27084339; PubMed Central PMCID: PMC4833930.

14. Hewing B, Landmesser U. LDL, HDL, VLDL, and CVD Prevention: Lessons from Genetics? Curr Cardiol Rep. 2015;17(7):610. Epub 2015/06/03. doi: 10.1007/s11886-015-0610-z 26031673.

15. Orho-Melander M. Genetics of coronary heart disease: towards causal mechanisms, novel drug targets and more personalized prevention. J Intern Med. 2015;278(5):433–46. Epub 2015/10/20. doi: 10.1111/joim.12407 26477595.

16. Patni N, Ahmad Z, Wilson DP. Genetics and Dyslipidemia. 2000. Epub 2016/11/05. doi: NBK395584 [bookaccession]. 27809445.

17. Ramasamy I. Update on the molecular biology of dyslipidemias. Clin Chim Acta. 2016;454:143–85. Epub 2015/11/08. doi: 10.1016/j.cca.2015.10.033 [pii]. 26546829.

18. Santos RD, Gidding SS, Hegele RA, Cuchel MA, Barter PJ, Watts GF, et al. Defining severe familial hypercholesterolaemia and the implications for clinical management: a consensus statement from the International Atherosclerosis Society Severe Familial Hypercholesterolemia Panel. Lancet Diabetes Endocrinol. 2016;4(10):850–61. Epub 2016/06/02. doi: 10.1016/S2213-8587(16)30041-9 [pii]. 27246162.

19. Wang LR, Hegele RA. Genetics for the Identification of Lipid Targets Beyond PCSK9. Can J Cardiol. 2017;33(3):334–42. Epub 2017/01/23. doi: S0828-282X(16)31088-1 [pii] doi: 10.1016/j.cjca.2016.11.003 28109622.

20. Wiegman A, Gidding SS, Watts GF, Chapman MJ, Ginsberg HN, Cuchel M, et al. Familial hypercholesterolaemia in children and adolescents: gaining decades of life by optimizing detection and treatment. Eur Heart J. 2015;36(36):2425–37. Epub 2015/05/27. doi: 10.1093/eurheartj/ehv157 [pii]. 26009596; PubMed Central PMCID: PMC4576143.

21. Cohen J, Pertsemlidis A, Kotowski IK, Graham R, Garcia CK, Hobbs HH. Low LDL cholesterol in individuals of African descent resulting from frequent nonsense mutations in PCSK9. Nat Genet. 2005;37(2):161–5. Epub 2005/01/18. doi: ng1509 [pii] doi: 10.1038/ng1509 15654334.

22. Cohen JC, Boerwinkle E, Mosley TH Jr., Hobbs HH. Sequence variations in PCSK9, low LDL, and protection against coronary heart disease. N Engl J Med. 2006;354(12):1264–72. Epub 2006/03/24. doi: 354/12/1264 [pii] doi: 10.1056/NEJMoa054013 16554528.

23. Fasano T, Cefalu AB, Di Leo E, Noto D, Pollaccia D, Bocchi L, et al. A novel loss of function mutation of PCSK9 gene in white subjects with low-plasma low-density lipoprotein cholesterol. Arterioscler Thromb Vasc Biol. 2007;27(3):677–81. Epub 2006/12/16. doi: 01.ATV.0000255311.26383.2f [pii] doi: 10.1161/01.ATV.0000255311.26383.2f 17170371.

24. Hallman DM, Srinivasan SR, Chen W, Boerwinkle E, Berenson GS. Relation of PCSK9 mutations to serum low-density lipoprotein cholesterol in childhood and adulthood (from The Bogalusa Heart Study). Am J Cardiol. 2007;100(1):69–72. Epub 2007/06/30. doi: S0002-9149(07)00575-9 [pii] doi: 10.1016/j.amjcard.2007.02.057 17599443.

25. Hooper AJ, Marais AD, Tanyanyiwa DM, Burnett JR. The C679X mutation in PCSK9 is present and lowers blood cholesterol in a Southern African population. Atherosclerosis. 2007;193(2):445–8. Epub 2006/09/23. doi: S0021-9150(06)00522-3 [pii] doi: 10.1016/j.atherosclerosis.2006.08.039 16989838.

26. Kotowski IK, Pertsemlidis A, Luke A, Cooper RS, Vega GL, Cohen JC, et al. A spectrum of PCSK9 alleles contributes to plasma levels of low-density lipoprotein cholesterol. Am J Hum Genet. 2006;78(3):410–22. Epub 2006/02/09. doi: S0002-9297(07)62381-7 [pii] doi: 10.1086/500615 16465619; PubMed Central PMCID: PMC1380285.

27. Miyake Y, Kimura R, Kokubo Y, Okayama A, Tomoike H, Yamamura T, et al. Genetic variants in PCSK9 in the Japanese population: rare genetic variants in PCSK9 might collectively contribute to plasma LDL cholesterol levels in the general population. Atherosclerosis. 2008;196(1):29–36. Epub 2007/02/24. doi: S0021-9150(07)00051-2 [pii] doi: 10.1016/j.atherosclerosis.2006.12.035 17316651.

28. Blom DJ, Hala T, Bolognese M, Lillestol MJ, Toth PD, Burgess L, et al. A 52-week placebo-controlled trial of evolocumab in hyperlipidemia. N Engl J Med. 2014;370(19):1809–19. Epub 2014/04/01. doi: 10.1056/NEJMoa1316222 24678979.

29. Cock PJa, Antao T, Chang JT, Chapman Ba, Cox CJ, Dalke A, et al. Biopython: Freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics. 2009;25(11):1422–3. doi: 10.1093/bioinformatics/btp163 19304878.

30. Dias CS, Shaywitz AJ, Wasserman SM, Smith BP, Gao B, Stolman DS, et al. Effects of AMG 145 on low-density lipoprotein cholesterol levels: results from 2 randomized, double-blind, placebo-controlled, ascending-dose phase 1 studies in healthy volunteers and hypercholesterolemic subjects on statins. J Am Coll Cardiol. 2012;60(19):1888–98. Epub 2012/10/23. doi: 10.1016/j.jacc.2012.08.986 [pii]. 23083772.

31. Raal FJ, Giugliano RP, Sabatine MS, Koren MJ, Langslet G, Bays H, et al. Reduction in lipoprotein(a) with PCSK9 monoclonal antibody evolocumab (AMG 145): a pooled analysis of more than 1,300 patients in 4 phase II trials. J Am Coll Cardiol. 2014;63(13):1278–88. Epub 2014/02/11. doi: 10.1016/j.jacc.2014.01.006 [pii]. 24509273.

32. Raal FJ, Stein EA, Dufour R, Turner T, Civeira F, Burgess L, et al. PCSK9 inhibition with evolocumab (AMG 145) in heterozygous familial hypercholesterolaemia (RUTHERFORD-2): a randomised, double-blind, placebo-controlled trial. Lancet. 2015;385(9965):331–40. Epub 2014/10/06. doi: 10.1016/S0140-6736(14)61399-4 [pii]. 25282519.

33. Stein EA, Honarpour N, Wasserman SM, Xu F, Scott R, Raal FJ. Effect of the proprotein convertase subtilisin/kexin 9 monoclonal antibody, AMG 145, in homozygous familial hypercholesterolemia. Circulation. 2013;128(19):2113–20. Epub 2013/09/10. doi: 10.1161/CIRCULATIONAHA.113.004678 [pii]. 24014831.

34. Stroes E, Colquhoun D, Sullivan D, Civeira F, Rosenson RS, Watts GF, et al. Anti-PCSK9 antibody effectively lowers cholesterol in patients with statin intolerance: the GAUSS-2 randomized, placebo-controlled phase 3 clinical trial of evolocumab. J Am Coll Cardiol. 2014;63(23):2541–8. Epub 2014/04/04. doi: 10.1016/j.jacc.2014.03.019 [pii]. 24694531.

35. Dufour R, Bergeron J, Gaudet D, Weiss R, Hovingh GK, Qing Z, et al. Open-label therapy with alirocumab in patients with heterozygous familial hypercholesterolemia: Results from three years of treatment. Int J Cardiol. 2017;228:754–60. Epub 2016/11/26. doi: S0167-5273(16)33493-3 [pii] doi: 10.1016/j.ijcard.2016.11.046 27886619.

36. Ginsberg HN, Rader DJ, Raal FJ, Guyton JR, Baccara-Dinet MT, Lorenzato C, et al. Efficacy and Safety of Alirocumab in Patients with Heterozygous Familial Hypercholesterolemia and LDL-C of 160 mg/dl or Higher. Cardiovasc Drugs Ther. 2016;30(5):473–83. Epub 2016/09/14. doi: 10.1007/s10557-016-6685-y [pii]. 27618825; PubMed Central PMCID: PMC5055560.

37. Kastelein JJ, Ginsberg HN, Langslet G, Hovingh GK, Ceska R, Dufour R, et al. ODYSSEY FH I and FH II: 78 week results with alirocumab treatment in 735 patients with heterozygous familial hypercholesterolaemia. Eur Heart J. 2015;36(43):2996–3003. Epub 2015/09/04. doi: 10.1093/eurheartj/ehv370 [pii]. 26330422; PubMed Central PMCID: PMC4644253.

38. Kereiakes DJ, Robinson JG, Cannon CP, Lorenzato C, Pordy R, Chaudhari U, et al. Efficacy and safety of the proprotein convertase subtilisin/kexin type 9 inhibitor alirocumab among high cardiovascular risk patients on maximally tolerated statin therapy: The ODYSSEY COMBO I study. Am Heart J. 2015;169(6):906–15 e13. Epub 2015/06/02. doi: 10.1016/j.ahj.2015.03.004 S0002-8703(15)00168-4 [pii]. 26027630.

39. Kuhnast S, van der Hoorn JW, Pieterman EJ, van den Hoek AM, Sasiela WJ, Gusarova V, et al. Alirocumab inhibits atherosclerosis, improves the plaque morphology, and enhances the effects of a statin. J Lipid Res. 2014;55(10):2103–12. Epub 2014/08/21. doi: 10.1194/jlr.M051326 [pii]. 25139399; PubMed Central PMCID: PMC4174003.

40. Robinson JG, Farnier M, Krempf M, Bergeron J, Luc G, Averna M, et al. Efficacy and safety of alirocumab in reducing lipids and cardiovascular events. N Engl J Med. 2015;372(16):1489–99. Epub 2015/03/17. doi: 10.1056/NEJMoa1501031 25773378.

41. Roth EM, Moriarty PM, Bergeron J, Langslet G, Manvelian G, Zhao J, et al. A phase III randomized trial evaluating alirocumab 300 mg every 4 weeks as monotherapy or add-on to statin: ODYSSEY CHOICE I. Atherosclerosis. 2016;254:254–62. Epub 2016/09/19. doi: S0021-9150(16)31311-9 [pii] doi: 10.1016/j.atherosclerosis.2016.08.043 27639753.

42. Roth EM, Taskinen MR, Ginsberg HN, Kastelein JJ, Colhoun HM, Robinson JG, et al. Monotherapy with the PCSK9 inhibitor alirocumab versus ezetimibe in patients with hypercholesterolemia: results of a 24 week, double-blind, randomized Phase 3 trial. Int J Cardiol. 2014;176(1):55–61. Epub 2014/07/20. doi: 10.1016/j.ijcard.2014.06.049 S0167-5273(14)01116-4 [pii]. 25037695.

43. Stroes E, Guyton JR, Lepor N, Civeira F, Gaudet D, Watts GF, et al. Efficacy and Safety of Alirocumab 150 mg Every 4 Weeks in Patients With Hypercholesterolemia Not on Statin Therapy: The ODYSSEY CHOICE II Study. J Am Heart Assoc. 2016;5(9). Epub 2016/09/15. doi: 10.1161/JAHA.116.003421e003421 [pii] JAHA.116.003421 [pii]. 27625344.

44. Taylor BA, Panza G, Pescatello LS, Chipkin S, Gipe D, Shao W, et al. Serum PCSK9 Levels Distinguish Individuals Who Do Not Respond to High-Dose Statin Therapy with the Expected Reduction in LDL-C. J Lipids. 2014;2014:140723. Epub 2014/08/20. doi: 10.1155/2014/140723 25136459; PubMed Central PMCID: PMC4127223.

45. Schmidt MW, Baldridge KK, Boatz JA, Elbert ST, Gordon MS, Jensen JH, et al. General atomic and molecular electronic structure system. Journal of Computational Chemistry. 1993;14(11):1347–63. doi: 10.1002/jcc.540141112

46. Leren TP. Sorting an LDL receptor with bound PCSK9 to intracellular degradation. Atherosclerosis. 2014;237(1):76–81. Epub 2014/09/16. doi: 10.1016/j.atherosclerosis.2014.08.038 [pii]. 25222343.

47. Tveten K, Holla OL, Cameron J, Strom TB, Berge KE, Laerdahl JK, et al. Interaction between the ligand-binding domain of the LDL receptor and the C-terminal domain of PCSK9 is required for PCSK9 to remain bound to the LDL receptor during endosomal acidification. Hum Mol Genet. 2012;21(6):1402–9. Epub 2011/12/14. doi: 10.1093/hmg/ddr578 [pii]. 22156580.

48. Guarnieri F, Mezei M. Simulated Annealing of Chemical Potential: A General Procedure for Locating Bound Waters. Application to the Study of the Differential Hydration Propensities of the Major and Minor Grooves of DNA. J Am Chem Soc. 1996;118(35):8493–94.

49. Guarnieri F. Computational Protein Probing to Identify Binding Sites. 2004;U.S. Patent 6735530.

50. Clark M, Guarnieri F, Shkurko I, Wiseman J. Grand canonical Monte Carlo simulation of ligand-protein binding. J Chem Inf Model. 2006;46(1):231–42. Epub 2006/01/24. doi: 10.1021/ci050268f 16426059.

51. Kulp JL 3rd, Cloudsdale IS, Kulp JL Jr., Guarnieri F. Hot-spot identification on a broad class of proteins and RNA suggest unifying principles of molecular recognition. PLoS One. 2017;12(8):e0183327. Epub 2017/08/25. doi: 10.1371/journal.pone.0183327 [pii]. 28837642; PubMed Central PMCID: PMC5570288.

52. Bradbury MW, Stump D, Guarnieri F, Berk PD. Molecular modeling and functional confirmation of a predicted fatty acid binding site of mitochondrial aspartate aminotransferase. J Mol Biol. 2011;412(3):412–22. Epub 2011/08/02. doi: S0022-2836(11)00799-6 [pii] doi: 10.1016/j.jmb.2011.07.034 21803047; PubMed Central PMCID: PMC3167029.

53. Kulp JL 3rd, Blumenthal SN, Wang Q, Bryan RL, Guarnieri F. A fragment-based approach to the SAMPL3 Challenge. J Comput Aided Mol Des. 2012;26(5):583–94. Epub 2012/02/01. doi: 10.1007/s10822-012-9546-1 22290624.

54. Kulp JL 3rd, Kulp JL Jr., Pompliano DL, Guarnieri F. Diverse fragment clustering and water exclusion identify protein hot spots. J Am Chem Soc. 2011;133(28):10740–3. Epub 2011/06/21. doi: 10.1021/ja203929x 21682273.

55. Vallee M, Vitiello S, Bellocchio L, Hebert-Chatelain E, Monlezun S, Martin-Garcia E, et al. Pregnenolone can protect the brain from cannabis intoxication. Science. 2014;343(6166):94–8. Epub 2014/01/05. doi: 10.1126/science.1243985 [pii]. 24385629; PubMed Central PMCID: PMC4057431.

56. Cloudsdale IS, Dickson JK Jr., Barta TE, Grella BS, Smith ED, Kulp JL 3rd, et al. Design, synthesis and biological evaluation of renin inhibitors guided by simulated annealing of chemical potential simulations. Bioorg Med Chem. 2017;25(15):3947–63. Epub 2017/06/12. doi: S0968-0896(17)30568-0 [pii] doi: 10.1016/j.bmc.2017.05.032 28601508; PubMed Central PMCID: PMC5553068.

57. Guarnieri F. Designing an Orally Available Nontoxic p38 Inhibitor with a Fragment-Based Strategy. Fragment-Based Methods in Drug Discovery; Klon Anthony, Editor. 2015;1289:211–26.

58. Guarnieri F. Designing a small molecule erythropoietin mimetic. Fragment-Based Methods in Drug Discovery; Klon Anthony, Editor. 2015;1289:185–210.

59. Guarnieri F. Analysis of the Asymmetry of Activated EPO Receptor Enables Designing Small Molecule Agonists. Vitam Horm. 2017;105:19–37. Epub 2017/06/21. doi: S0083-6729(17)30025-0 [pii] doi: 10.1016/bs.vh.2017.03.004 28629518.

60. Moffett K, Konteatis Z, Nguyen D, Shetty R, Ludington J, Fujimoto T, et al. Discovery of a novel class of non-ATP site DFG-out state p38 inhibitors utilizing computationally assisted virtual fragment-based drug design (vFBDD). Bioorg Med Chem Lett. 2011;21(23):7155–65. Epub 2011/10/22. doi: S0960-894X(11)01322-9 [pii] doi: 10.1016/j.bmcl.2011.09.078 22014550.

61. Kirkpatrick S, Gelatt CD Jr., Vecchi MP. Optimization by simulated annealing. Science. 1983;220(4598):671–80. Epub 1983/05/13. doi: 220/4598/671 [pii] doi: 10.1126/science.220.4598.671 17813860.

62. Chung F, Tisne C, Lecourt T, Seijo B, Dardel F, Micouin L. Design of tRNA(Lys)3 ligands: fragment evolution and linker selection guided by NMR spectroscopy. Chemistry. 2009;15(29):7109–16. Epub 2009/06/23. doi: 10.1002/chem.200802451 19544516.

63. Chung S, Parker JB, Bianchet M, Amzel LM, Stivers JT. Impact of linker strain and flexibility in the design of a fragment-based inhibitor. Nat Chem Biol. 2009;5(6):407–13. Epub 2009/04/28. doi: 10.1038/nchembio.163 [pii]. 19396178; PubMed Central PMCID: PMC3178264.

64. Jahnke W, Florsheimer A, Blommers MJ, Paris CG, Heim J, Nalin CM, et al. Second-site NMR screening and linker design. Curr Top Med Chem. 2003;3(1):69–80. Epub 2003/02/07. doi: 10.2174/1568026033392778 12570778.

65. Ranjan N, Kellish P, King A, Arya DP. Impact of Linker Length and Composition on Fragment Binding and Cell Permeation: Story of a Bisbenzimidazole Dye Fragment. Biochemistry. 2017;56(49):6434–47. Epub 2017/11/14. doi: 10.1021/acs.biochem.7b00929 29131946.

66. Zhou Y, Zhang N, Qi X, Tang S, Sun G, Zhao L, et al. Insights into the Impact of Linker Flexibility and Fragment Ionization on the Design of CK2 Allosteric Inhibitors: Comparative Molecular Dynamics Simulation Studies. Int J Mol Sci. 2018;19(1). Epub 2018/01/06. doi: E111 [pii] doi: 10.3390/ijms19010111 ijms19010111 [pii]. 29301250; PubMed Central PMCID: PMC5796060.

67. Boyer RD, Bryan RL. Fast estimation of solvation free energies for diverse chemical species. J Phys Chem B. 2012;116(12):3772–9. Epub 2012/02/22. doi: 10.1021/jp300440d 22339050

68. Bottomley MJ, Cirillo A, Orsatti L, Ruggeri L, Fisher TS, Santoro JC, et al. Structural and biochemical characterization of the wild type PCSK9-EGF(AB) complex and natural familial hypercholesterolemia mutants. J Biol Chem. 2009;284(2):1313–23. Epub 2008/11/13. doi: 10.1074/jbc.M808363200 [pii]. 19001363.

69. Golunski G, Borowik A, Derewonko N, Kawiak A, Rychlowski M, Woziwodzka A, et al. Pentoxifylline as a modulator of anticancer drug doxorubicin. Part II: Reduction of doxorubicin DNA binding and alleviation of its biological effects. Biochimie. 2016;123:95–102. Epub 2016/02/09. doi: 10.1016/j.biochi.2016.02.003 [pii]. 26855172.

70. Hartlieb KJ, Witus LS, Ferris DP, Basuray AN, Algaradah MM, Sarjeant AA, et al. Anticancer activity expressed by a library of 2,9-diazaperopyrenium dications. ACS Nano. 2015;9(2):1461–70. Epub 2015/01/03. doi: 10.1021/nn505895j 25555133; PubMed Central PMCID: PMC4344210.

71. Stornaiuolo M, De Kloe GE, Rucktooa P, Fish A, van Elk R, Edink ES, et al. Assembly of a pi-pi stack of ligands in the binding site of an acetylcholine-binding protein. Nat Commun. 2013;4:1875. Epub 2013/05/23. doi: 10.1038/ncomms2900 [pii]. 23695669; PubMed Central PMCID: PMC3674282.

72. Hahn L, Lubtow MM, Lorson T, Schmitt F, Appelt-Menzel A, Schobert R, et al. Investigating the Influence of Aromatic Moieties on the Formulation of Hydrophobic Natural Products and Drugs in Poly(2-oxazoline)-Based Amphiphiles. Biomacromolecules. 2018. Epub 2018/05/11. doi: 10.1021/acs.biomac.8b00708 29746117.

73. Li S, Zhou S, Li Y, Li X, Zhu J, Fan L, et al. Exceptionally High Payload of the IR780 Iodide on Folic Acid-Functionalized Graphene Quantum Dots for Targeted Photothermal Therapy. ACS Appl Mater Interfaces. 2017;9(27):22332–41. Epub 2017/06/24. doi: 10.1021/acsami.7b07267 28643511.

74. Yang X, Xue X, Luo Y, Lin TY, Zhang H, Lac D, et al. Sub-100nm, long tumor retention SN-38-loaded photonic micelles for tri-modal cancer therapy. J Control Release. 2017;261:297–306. Epub 2017/07/13. doi: S0168-3659(17)30722-8 [pii] doi: 10.1016/j.jconrel.2017.07.014 28700898; PubMed Central PMCID: PMC5589441.

75. Zhu S, Gao H, Babu S, Garad S. Co-Amorphous Formation of High-Dose Zwitterionic Compounds with Amino Acids To Improve Solubility and Enable Parenteral Delivery. Mol Pharm. 2018;15(1):97–107. Epub 2017/11/23. doi: 10.1021/acs.molpharmaceut.7b00738 29164901.

76. Taechalertpaisarn J, Zhao B, Liang X, Burgess K. Small Molecule Inhibitors of the PCSK9.LDLR Interaction. J Am Chem Soc. 2018;140(9):3242–9. Epub 2018/01/31. doi: 10.1021/jacs.7b09360 29378408; PubMed Central PMCID: PMC6404525.

77. Ni YG, Condra JH, Orsatti L, Shen X, Di Marco S, Pandit S, et al. A proprotein convertase subtilisin-like/kexin type 9 (PCSK9) C-terminal domain antibody antigen-binding fragment inhibits PCSK9 internalization and restores low density lipoprotein uptake. J Biol Chem. 2010;285(17):12882–91. Epub 2010/02/23. doi: 10.1074/jbc.M110.113035 [pii]. 20172854; PubMed Central PMCID: PMC2857140.

78. Zhang Y, Eigenbrot C, Zhou L, Shia S, Li W, Quan C, et al. Identification of a small peptide that inhibits PCSK9 protein binding to the low density lipoprotein receptor. J Biol Chem. 2014;289(2):942–55. Epub 2013/11/15. doi: 10.1074/jbc.M113.514067 [pii]. 24225950; PubMed Central PMCID: PMC3887217.

79. Fisher TS, Lo Surdo P, Pandit S, Mattu M, Santoro JC, Wisniewski D, et al. Effects of pH and low density lipoprotein (LDL) on PCSK9-dependent LDL receptor regulation. J Biol Chem. 2007;282(28):20502–12. Epub 2007/05/12. doi: M701634200 [pii] doi: 10.1074/jbc.M701634200 17493938.

Článek vyšel v časopise


2019 Číslo 12
Nejčtenější tento týden