SQM/COSMO Scoring Function: Reliable Quantum-Mechanical Tool for Sampling and Ranking in Structure-Based Drug Design

. 2020 Nov ; 85 (11) : 2362-2371. [epub] 20200701

Jazyk angličtina Země Německo Médium print-electronic

Typ dokumentu časopisecké články, práce podpořená grantem, přehledy

Perzistentní odkaz   https://www.medvik.cz/link/pmid32609421

Quantum mechanical (QM) methods have been gaining importance in structure-based drug design where a reliable description of protein-ligand interactions is of utmost significance. However, strategies i. e. QM/MM, fragmentation or semiempirical (SQM) methods had to be pursued to overcome the unfavorable scaling of QM methods. Various SQM-based approaches have significantly contributed to the accuracy of docking and improvement of lead compounds. Parametrizations of SQM and implicit solvent methods in our laboratory have been instrumental to obtain a reliable SQM-based scoring function. The experience gained in its application for activity ranking of ligands binding to tens of protein targets resulted in setting up a faster SQM/COSMO scoring approach, which outperforms standard scoring methods in native pose identification for two dozen protein targets with ten thousand poses. Recently, SQM/COSMO was effectively applied in a proof-of-concept study of enrichment in virtual screening. Due to its superior performance, feasibility and chemical generality, we propose the SQM/COSMO approach as an efficient tool in structure-based drug design.

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G. Klebe, Drug Discovery Today 2006, 11, 580-594;

G. Schneider, Nat. Rev. Drug Discovery 2010, 9, 273-276.

D. C. Young, Computational Drug Design: A Guide for Computational and Medicinal Chemists, John Wiley & Sons, Inc., 2009.

J. J. Irwin, B. K. Shoichet, J. Med. Chem. 2016, 59, 4103-4120.

L. Pinzi, G. Rastelli, Int. J. Mol. Sci. 2019, 20, e4331.

E. Yuriev, J. Holien, P. A. Ramsland, J. Mol. Recognit. 2015, 28, 581-604;

C. F. Wong, Expert Opin. Drug Discovery 2015, 10, 1189-1200;

M. De Vivo, M. Masetti, G. Bottegoni, A. Cavalli, J. Med. Chem. 2016, 59, 4035-4061;

D. Gioia, M. Bertazzo, M. Recanatini, M. Masetti, A. Cavalli, Molecules 2017, 22, 2029-2050;

N. J. Bruce, G. K. Ganotra, D. B. Kokh, S. K. Sadiq, R. C. Wade, Curr. Opin. Struct. Biol. 2018, 49, 1-10;

P. Sledz, A. Caflisch, Curr. Opin. Struct. Biol. 2018, 48, 93-102;

R. E. Amaro, J. Baudry, J. Chodera, O. Demir, J. A. McCammon, Y. Miao, J. C. Smith, Biophys. J. 2018, 114, 2271-2278;

V. B. Sulimov, D. C. Kutov, A. V. Sulimov, Curr. Med. Chem. 2019, 26, 7555-7580;

Z. Wang, H. Sun, C. Shen, X. Hu, J. Gao, D. Li, D. Cao, T. Hou, Phys. Chem. Chem. Phys. 2020, 22, 3149-3159.

M. Kolar, J. Fanfrlik, M. Lepsik, F. Forti, F. J. Luque, P. Hobza, J. Phys. Chem. B 2013, 117, 5950-5962;

S. Decherchi, M. Masetti, I. Vyalov, W. Rocchia, Eur. J. Med. Chem. 2015, 91, 27-42.

R. A. Friesner, R. B. Murphy, M. P. Repasky, L. L. Frye, J. R. Greenwood, T. A. Halgren, P. C. Sanschagrin, D. T. Mainz, J. Med. Chem. 2006, 49, 6177-6196;

T. Beuming, Y. Che, R. Abel, B. Kim, V. Shanmugasundaram, W. Sherman, Proteins 2012, 80, 871-883;

B. Vorlova, D. Nachtigallova, J. Jiraskova-Vanickova, H. Ajani, P. Jansa, J. Rezac, J. Fanfrlik, M. Otyepka, P. Hobza, J. Konvalinka, M. Lepsik, Eur. J. Med. Chem. 2015, 89, 189-197;

J. M. Fox, K. Kang, M. Sastry, W. Sherman, B. Sankaran, P. H. Zwart, G. M. Whitesides, Angew. Chem. Int. Ed. 2017, 56, 3833-3837;

Angew. Chem. 2017, 129, 3891-3895;

M. Hylsova, B. Carbain, J. Fanfrlik, L. Musilova, S. Haldar, C. Kopruluoglu, H. Ajani, P. S. Brahmkshatriya, R. Jorda, V. Krystof, P. Hobza, A. Echalier, K. Paruch, M. Lepsik, Eur. J. Med. Chem. 2017, 126, 1118-1128.

X. Yang, Y. Wang, R. Byrne, G. Schneider, S. Yang, Chem. Rev. 2019, 119, 10520-10594;

K. H. S. Hongjian Li, Gang Lu, Pedro J. Ballester, Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2020, 17, e1465.

A. Ciancetta, S. Genheden, U. Ryde, J. Comput.-Aided Mol. Des. 2011, 25, 729-742;

J. Fanfrlik, P. S. Brahmkshatriya, J. Rezac, A. Jilkova, M. Horn, M. Mares, P. Hobza, M. Lepsik, J. Phys. Chem. B 2013, 117, 14973-14982.

M. B. Peters, K. Raha, K. M. Merz Jr., Curr. Opin. Drug Discovery Dev. 2006, 9, 370-379;

A. Cavalli, P. Carloni, M. Recanatini, Chem. Rev. 2006, 106, 3497-3519;

K. Raha, M. B. Peters, B. Wang, N. Yu, A. M. WollaCott, L. M. Westerhoff, K. M. Merz, Drug Discovery Today 2007, 12, 725-731;

P. Soderhjelm, J. Kongsted, U. Ryde, J. Chem. Theory Comput. 2010, 6, 1726-1737;

Y. Q. Jing, K. L. Han, Expert Opin. Drug Discovery 2010, 5, 33-49;

T. Zhou, D. Z. Huang, A. Caflisch, Curr. Top. Med. Chem. 2010, 10, 33-45;

D. Mucs, R. A. Bryce, Expert Opin. Drug Discovery 2013, 8, 263-276;

J. H. Jensen, Phys. Chem. Chem. Phys. 2015, 17, 12441-12451;

U. Ryde, P. Soderhjelm, Chem. Rev. 2016, 116, 5520-5566;

N. D. Yilmazer, M. Korth, Int. J. Mol. Sci. 2016, 17, 742-755;

A. A. Adeniyi, M. E. S. Soliman, Drug Discovery Today 2017, 22, 1216-1223;

A. Crespo, A. Rodriguez-Granillo, V. T. Lim, Curr. Top. Med. Chem. 2017, 17, 2663-2680;

C. N. Cavasotto, N. S. Adler, M. G. Aucar, Front. Chem. 2018, 6, 188;

A. Heifetz, Quantum Mechanics in Drug Discovery, Humana, New York, NY, New York, USA, 2020;

M. Kotev, L. Sarrat, C. D. Gonzalez, Methods Mol. Biol. 2020, 2114, 231-255;

R. A. Bryce, Methods Mol. Biol. 2020, 2114, 339-353.

J. Rezac, P. Hobza, Chem. Rev. 2016, 116, 5038-5071;

M. H. Kolar, P. Hobza, Chem. Rev. 2016, 116, 5155-5187;

P. Politzer, J. S. Murray, T. Clark, G. Resnati, Phys. Chem. Chem. Phys. 2017, 19, 32166-32178.

J. Fanfrlik, M. Kolar, M. Kamlar, D. Hurny, F. X. Ruiz, A. Cousido-Siah, A. Mitschler, J. Rezac, E. Munusamy, M. Lepsik, P. Matejicek, J. Vesely, A. Podjarny, P. Hobza, ACS Chem. Biol. 2013, 8, 2484-2492;

J. Fanfrlik, F. X. Ruiz, A. Kadlcikova, J. Rezac, A. Cousido-Siah, A. Mitschler, S. Haldar, M. Lepsik, M. H. Kolar, P. Majer, A. D. Podjarny, P. Hobza, ACS Chem. Biol. 2015, 10, 1637-1642;

K. Kriz, J. Fanfrlik, M. Lepsik, ChemPhysChem 2018, 19, 2540-2548.

M. J. Field, P. A. Bash, M. Karplus, J. Comput. Chem. 1990, 11, 700-733;

H. M. Senn, W. Thiel, Angew. Chem. Int. Ed. 2009, 48, 1198-1229;

Angew. Chem. 2009, 121, 1220-1254;

L. C. Menikarachchi, J. A. Gascon, Curr. Top. Med. Chem. 2010, 10, 46-54;

S. K. Burger, D. C. Thompson, P. W. Ayers, J. Chem. Inf. Model. 2011, 51, 93-101;

J. Antony, S. Grimme, D. G. Liakos, F. Neese, J. Phys. Chem. A 2011, 115, 11210-11220;

R. A. Bryce, I. H. Hillier, Curr. Pharm. Des. 2014, 20, 3293-3302;

S. Ahmadi, L. B. Herrera, M. Chehelamirani, J. Hostas, S. Jalife, D. R. Salahub, Int. J. Quantum Chem. 2018, 118, e25558.

J. Rezac, J. Fanfrlik, D. Salahub, P. Hobza, J. Chem. Theory Comput. 2009, 5, 1749-1760;

M. Korth, M. Pitonak, J. Rezac, P. Hobza, J. Chem. Theory Comput. 2010, 6, 344-352;

J. Rezac, P. Hobza, Chem. Phys. Lett. 2011, 506, 286-289;

J. Rezac, P. Hobza, J. Chem. Theory Comput. 2012, 8, 141-151;

A. S. Christensen, T. Kubar, Q. Cui, M. Elstner, Chem. Rev. 2016, 116, 5301-5337.

M. Lepsik, J. Rezac, M. Kolar, A. Pecina, P. Hobza, J. Fanfrlik, ChemPlusChem 2013, 78, 921-931.

A. Pecina, R. Meier, J. Fanfrlik, M. Lepsik, J. Rezac, P. Hobza, C. Baldauf, Chem. Commun. 2016, 52, 3312-3315;

A. Pecina, S. Haldar, J. Fanfrlik, R. Meier, J. Rezac, M. Lepsik, P. Hobza, J. Chem. Inf. Model. 2017, 57, 127-132;

H. Ajani, A. Pecina, S. M. Eyrilmez, J. Fanfrlik, S. Haldar, J. Rezac, P. Hobza, M. Lepsik, ACS Omega 2017, 2, 4022-4029;

A. Pecina, J. Brynda, L. Vrzal, R. Gnanasekaran, M. Horejsi, S. M. Eyrilmez, J. Rezac, M. Lepsik, P. Rezacova, P. Hobza, P. Majer, V. Veverka, J. Fanfrlik, ChemPhysChem 2018, 19, 873-879;

S. M. Eyrilmez, C. Kopruluoglu, J. Rezac, P. Hobza, ChemPhysChem 2019, 20, 2759-2766.

W. T. Michael, J. S. Dewart, J. Am. Chem. Soc. 1977, 99, 4899-4907;

M. J. S. Dewar, E. G. Zoebisch, E. F. Healy, J. J. P. Stewart, J. Am. Chem. Soc. 1985, 107, 3902-3909;

J. J. P. Stewart, J. Comput. Chem. 1991, 12, 320-341;

W. Weber, W. Thiel, Theor. Chem. Acc. 2000, 103, 495-506;

J. J. P. Stewart, J. Mol. Model. 2007, 13, 1173-1213;

J. J. P. Stewart, J. Mol. Model. 2013, 19, 1-32;

P. O. Dral, X. Wu, L. Sporkel, A. Koslowski, W. Weber, R. Steiger, M. Scholten, W. Thiel, J. Chem. Theory Comput. 2016, 12, 1082-1096;

P. O. Dral, X. Wu, W. Thiel, J. Chem. Theory Comput. 2019, 15, 1743-1760.

M. Elstner, P. Hobza, T. Frauenheim, S. Suhai, E. Kaxiras, J. Chem. Phys. 2001, 114, 5149-5155.

S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput. 2017, 13, 1989-2009;

C. Bannwarth, S. Ehlert, S. Grimme, J. Chem. Theory Comput. 2019, 15, 1652-1671.

M. Gaus, Q. A. Cui, M. Elstner, J. Chem. Theory Comput. 2011, 7, 931-948;

M. Gaus, X. Y. Lu, M. Elstner, Q. Cui, J. Chem. Theory Comput. 2014, 10, 1518-1537;

M. Kubillus, T. Kubar, M. Gaus, J. Rezac, M. Elstner, J. Chem. Theory Comput. 2015, 11, 332-342;

X. Y. Lu, M. Gaus, M. Elstner, Q. Cui, J. Phys. Chem. B 2015, 119, 1062-1082.

J. J. P. Stewart, Int. J. Quantum Chem. 1996, 58, 133-146.

W. T. Yang, T. S. Lee, J. Chem. Phys. 1995, 103, 5674-5678;

Y. Nishimura, H. Nakai, J. Comput. Chem. 2018, 39, 105-116.

J. P. McNamara, I. H. Hillier, Phys. Chem. Chem. Phys. 2007, 9, 2362-2370;

T. Tuttle, W. Thiel, Phys. Chem. Chem. Phys. 2008, 10, 2159-2166;

S. Grimme, A. Hansen, J. G. Brandenburg, C. Bannwarth, Chem. Rev. 2016, 116, 5105-5154.

P. Jurecka, J. Cerny, P. Hobza, D. R. Salahub, J. Comput. Chem. 2007, 28, 555-569;

J. Antony, S. Grimme, Phys. Chem. Chem. Phys. 2006, 8, 5287-5293.

J. Rezac, J. Chem. Theory Comput. 2017, 13, 4804-4817;

V. M. Miriyala, J. Rezac, J. Comput. Chem. 2017, 38, 688-697.

J. Rezac, J. Comput. Chem. 2019, 40, 1633-1642.

J. Rezac, P. Hobza, J. Chem. Theory Comput. 2013, 9, 2151-2155.

J. Rezac, J. Comput. Chem. 2016, 37, 1230-1237.

J. J. P. Stewart, HTTP://OpenMOPAC.net ed., Stewart Computational Chemistry, Colorado Springs, CO, USA, 2016.

B. Aradi, B. Hourahine, T. Frauenheim, J. Phys. Chem. A 2007, 111, 5678-5684.

K. Kriz, J. Rezac, J. Chem. Inf. Model. 2020, 60, 1453-1460.

J. Hostas, J. Rezac, P. Hobza, Chem. Phys. Lett. 2013, 568, 161-166.

V. Tsui, D. A. Case, Biopolymers 2001, 56, 275-291.

B. Honig, K. Sharp, A. S. Yang, J. Phys. Chem. 1993, 97, 1101-1109.

C. Curutchet, M. Orozco, F. J. Luque, J. Comput. Chem. 2001, 22, 1180-1193;

I. Soteras, C. Curutchet, A. Bidon-Chanal, M. Orozco, F. J. Luque, J. Mol. Struct.: THEOCHEM 2005, 727, 29-40.

A. V. Marenich, C. J. Cramer, D. G. Truhlar, J. Phys. Chem. B 2009, 113, 6378-6396.

A. Klamt, Abstr. Pap. Am. Chem. Soc. 1995, 210, 122-COMP.

A. Klamt, G. Schuurmann, J. Chem. Soc. Perkin Trans. 2 1993, 799-805.

K. Kriz, J. Rezac, J. Chem. Inf. Model. 2019, 59, 229-235.

D. L. Mobley, P. V. Klimovich, J. Chem. Phys. 2012, 137, 230901;

N. Hansen, W. F. van Gunsteren, J. Chem. Theory Comput. 2014, 10, 2632-2647;

D. L. Mobley, M. K. Gilson, Annu. Rev. Biophys. 2017, 46, 531-558.

W. Wang, O. Donini, C. M. Reyes, P. A. Kollman, Annu. Rev. Biophys. 2001, 30, 211-243;

M. R. Shirts, J. W. Pitera, W. C. Swope, V. S. Pande, J. Chem. Phys. 2003, 119, 5740-5761;

M. Karplus, Annu. Rev. Biophys. 2006, 35, 1-47;

M. K. Gilson, H. X. Zhou, Annu. Rev. Biophys. 2007, 36, 21-42;

M. Goette, H. Grubmuller, J. Comput. Chem. 2009, 30, 447-456;

W. L. Jorgensen, Acc. Chem. Res. 2009, 42, 724-733;

N. Singh, A. Warshel, Proteins 2010, 78, 1705-1723.

M. R. Reddy, M. D. Erion, J. Am. Chem. Soc. 2007, 129, 9296-9297;

M. R. Reddy, U. C. Singh, M. D. Erion, J. Am. Chem. Soc. 2011, 133, 8059-8061;

K. Swiderek, S. Marti, V. Moliner, Phys. Chem. Chem. Phys. 2012, 14, 12614-12624;

M. A. Olsson, P. Soderhjelm, U. Ryde, J. Comput. Chem. 2016, 37, 1589-1600;

C. Pu, G. Yan, J. Shi, R. Li, MedChemComm 2017, 8, 1452-1458;

Z. Sun, Phys. Chem. Chem. Phys. 2019, 21, 21942-21959;

D. J. Cole, I. Cabeza de Vaca, W. L. Jorgensen, MedChemComm 2019, 10, 1116-1120.

F. S. Lee, Z. T. Chu, M. B. Bolger, A. Warshel, Protein Eng. 1992, 5, 215-228;

J. Aqvist, C. Medina, J. E. Samuelsson, Protein Eng. 1994, 7, 385-391.

P. A. Kollman, I. Massova, C. Reyes, B. Kuhn, S. H. Huo, L. Chong, M. Lee, T. Lee, Y. Duan, W. Wang, O. Donini, P. Cieplak, J. Srinivasan, D. A. Case, T. E. Cheatham, Acc. Chem. Res. 2000, 33, 889-897;

H. Gohlke, D. A. Case, J. Comput. Chem. 2004, 25, 238-250.

C. N. Alves, S. Marti, R. Castillo, J. Andres, V. Moliner, I. Tunon, E. Silla, Chem. Eur. J. 2007, 13, 7715-7724;

J. H. Alzate-Morales, R. Contreras, A. Soriano, I. Tunon, E. Silla, Biophys. J. 2007, 92, 430-439;

T. Zhou, D. Huang, A. Caflisch, J. Med. Chem. 2008, 51, 4280-4288;

M. Xiang, Y. Lin, G. He, L. Chen, M. Yang, S. Yang, Y. Mo, J. Mol. Model. 2012, 18, 4917-4927;

E. H. Frush, S. Sekharan, S. Keinan, J. Phys. Chem. B 2017, 121, 8142-8148.

B. Kuhn, P. A. Kollman, J. Med. Chem. 2000, 43, 3786-3791;

S. Genheden, U. Ryde, J. Comput. Chem. 2010, 31, 837-846.

N. Diaz, D. Suarez, K. M. Merz, Jr., T. L. Sordo, J. Med. Chem. 2005, 48, 780-791;

R. C. Walker, M. F. Crowley, D. A. Case, J. Comput. Chem. 2008, 29, 1019-1031;

V. M. Anisimov, C. N. Cavasotto, J. Comput. Chem. 2011, 32, 2254-2263;

V. M. Anisimov, A. Ziemys, S. Kizhake, Z. Yuan, A. Natarajan, C. N. Cavasotto, J. Comput.-Aided Mol. Des. 2011, 25, 1071-1084;

P. Mikulskis, S. Genheden, K. Wichmann, U. Ryde, J. Comput. Chem. 2012, 33, 1179-1189;

K. Wichapong, A. Rohe, C. Platzer, I. Slynko, F. Erdmann, M. Schmidt, W. Sippl, J. Chem. Inf. Model. 2014, 54, 881-893;

L. D. Alvarez, A. S. Veleiro, G. Burton, Proteins 2015, 83, 1297-1306.

F. Grater, S. M. Schwarzl, A. Dejaegere, S. Fischer, J. C. Smith, J. Phys. Chem. B 2005, 109, 10474-10483;

M. Retegan, A. Milet, H. Jamet, J. Chem. Inf. Model. 2009, 49, 963-971;

Y. T. Wang, Y. C. Chen, Mol. Inf. 2014, 33, 240-249;

J. Lu, Z. Zhang, Z. Ni, H. Shen, Z. Tu, H. Liu, R. Lu, Comput. Biol. Chem. 2014, 52, 25-33;

J. Chen, J. Wang, Q. Zhang, K. Chen, W. Zhu, J. Biomol. Struct. Dyn. 2015, 33, 2606-2618;

E. C. M. Nascimento, M. Oliva, K. Swiderek, J. B. L. Martins, J. Andres, J. Chem. Inf. Model. 2017, 57, 958-976;

C. Steinmann, M. A. Olsson, U. Ryde, J. Chem. Theory Comput. 2018, 14, 3228-3237.

F. Beierlein, H. Lanig, G. Schürer, A. H. C. Horn, T Clark, Mol. Phys. 2003, 101, 2469-2480.

V. B. Vasilyev, Theor. Chem. Acc. 2004, 112, 313-317.

E. Nikitina, D. Sulimov, V. Zayets, N. Zaitseva, Int. J. Quantum Chem. 2004, 97, 747-763.

K. Raha, K. M. Merz, J. Am. Chem. Soc. 2004, 126, 1020-1021.

K. Raha, K. M. Merz, J. Med. Chem. 2005, 48, 4558-4575;

S. A. Hayik, R. Dunbrack, K. M. Merz, J. Chem. Theory Comput. 2010, 6, 3079-3091.

H. S. Muddana, M. K. Gilson, J. Chem. Theory Comput. 2012, 8, 2023-2033.

M. N. Ucisik, Z. Zheng, J. C. Faver, K. M. Merz, J. Chem. Theory Comput. 2014, 10, 1314-1325.

G. Nagy, B. Gyurcsik, E. A. Hoffmann, T. Kortvelyesi, J. Mol. Graphics Modell. 2011, 29, 928-934;

M. L. Benson, J. C. Faver, M. N. Ucisik, D. S. Dashti, Z. Zheng, K. M. Merz, Jr., J. Comput.-Aided Mol. Des. 2012, 26, 647-659;

K. Kamel, A. Kolinski, Acta Biochim. Pol. 2012, 59, 653-660;

J. L. Stigliani, V. Bernardes-Genisson, J. Bernadou, G. Pratviel, Org. Biomol. Chem. 2012, 10, 6341-6349;

L. Rao, I. Y. Zhang, W. P. Guo, L. Feng, E. Meggers, X. Xu, J. Comput. Chem. 2013, 34, 1636-1646;

C. Barberot, J. C. Boisson, S. Gerard, H. Khartabil, E. Thiriot, G. Monard, E. Henon, Comput. Theor. Chem. 2014, 1028, 7-18;

G. A. Urquiza-Carvalho, W. D. Fragoso, G. B. Rocha, J. Comput. Chem. 2016, 37, 1962-1972.

C. A. Ortiz-Mahecha, H. J. Bohorquez, W. A. Agudelo, M. A. Patarroyo, M. E. Patarroyo, C. F. Suarez, J. Chem. Inf. Model. 2019, 59, 5148-5160.

B. R. Brooks, C. L. Brooks, 3rd, A. D. Mackerell, Jr., L. Nilsson, R. J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Yang, D. M. York, M. Karplus, J. Comput. Chem. 2009, 30, 1545-1614.

P. Chaskar, V. Zoete, U. F. Rohrig, J. Chem. Inf. Model. 2014, 54, 3137-3152.

V. Zoete, T. Schuepbach, C. Bovigny, P. Chaskar, A. Daina, U. F. Rohrig, O. Michielin, J. Comput. Chem. 2016, 37, 437-447.

M. S. Gordon, D. G. Fedorov, S. R. Pruitt, L. V. Slipchenko, Chem. Rev. 2012, 112, 632-672;

J. F. Liu, X. W. Wang, J. Z. H. Zhang, X. He, RSC Adv. 2015, 5, 107020-107030.

T. Zhou, A. Caflisch, ChemMedChem 2010, 5, 1007-1014;

B. Thapa, D. Beckett, J. Erickson, K. Raghavachari, J. Chem. Theory Comput. 2018, 14, 5143-5155.

C. Esposito, L. Wiedmer, A. Caflisch, J. Chem. Inf. Model. 2018, 58, 2151-2163.

J. Fanfrlik, A. K. Bronowska, J. Rezac, O. Prenosil, J. Konvalinka, P. Hobza, J. Phys. Chem. B 2010, 114, 12666-12678.

J. Snasel, P. Naus, J. Dostal, A. Hnizda, J. Fanfrlik, J. Brynda, A. Bourderioux, M. Dusek, H. Dvorakova, J. Stolarikova, H. Zabranska, R. Pohl, P. Konecny, P. Dzubak, I. Votruba, M. Hajduch, P. Rezacova, V. Veverka, M. Hocek, I. Pichova, J. Med. Chem. 2014, 57, 8268-8279;

M. Nekardova, L. Vymetalova, P. Khirsariya, S. Kovacova, M. Hylsova, R. Jorda, V. Krystof, J. Fanfrlik, P. Hobza, K. Paruch, ChemPhysChem 2017, 18, 785-795;

H. Ajani, J. Jansa, C. Kopruluoglu, P. Hobza, V. Krystof, A. Lycka, M. Lepsik, J. Mol. Recognit. 2018, 31, e2720;

C. Köprülüoğlu, M. Dejmek, M. Šála, H. Ajani, H. Hřebabecký, J. Fanfrlík, R. Jorda, M. Dračínský, E. Procházková, B. Klepetářová, P. Šácha, V. Kryštof, P. Hobza, M. Lepšík, R. Nencka, J. Mol. Recognit. 2020, e2842.

R. Houstecka, M. Hadzima, J. Fanfrlik, J. Brynda, L. Pallova, I. Hanova, H. Mertlikova-Kaiserova, M. Lepsik, M. Horn, M. Smrčina, P. Majer, M. Mares, J. Med. Chem. 2020, 4, 1576-1596;

J. Dostal, A. Pecina, O. Hruskova-Heidingsfeldova, L. Mareckova, I. Pichova, P. Rezacova, M. Lepsik, J. Brynda, Acta Crystallogr. Sect. D 2015, 71, 2494-2504.

A. Cousido-Siah, F. X. Ruiz, J. Fanfrlik, J. Gimenez-Dejoz, A. Mitschler, M. Kamlar, J. Vesely, H. Ajani, X. Pares, J. Farres, P. Hobza, A. D. Podjarny, ACS Chem. Biol. 2016, 11, 2693-2705.

H. Cahova, A. Panattoni, P. Kielkowski, J. Fanfrlik, M. Hocek, ACS Chem. Biol. 2016, 11, 3165-3171.

L. Zakova, E. Kletvikova, M. Lepsik, M. Collinsova, C. J. Watson, J. P. Turkenburg, J. Jiracek, A. M. Brzozowski, Acta Crystallogr. Sect. D 2014, 70, 2765-2774.

J. Gemperle, R. Hexnerova, M. Lepsik, P. Tesina, M. Dibus, M. Novotny, J. Brabek, V. Veverka, D. Rosel, Sci. Rep. 2017, 7, 8057.

A. Pecina, M. Lepsik, J. Rezac, J. Brynda, P. Mader, P. Rezacova, P. Hobza, J. Fanfrlik, J. Phys. Chem. B 2013, 117, 16096-16104.

P. Mader, A. Pecina, P. Cigler, M. Lepsik, V. Sicha, P. Hobza, B. Gruner, J. Fanfrlik, J. Brynda, P. Rezacova, BioMed Res. Int. 2014, 389896.

D. E. Honda, J. B. L. Martins, M. M. Ventura, S. M. Eyrilmez, M. Lepsik, P. Hobza, A. Pecina, S. M. de Freitas, Eur. J. Org. Chem. 2018, 2018, 5203-5211.

Y. Duan, C. Wu, S. Chowdhury, M. C. Lee, G. M. Xiong, W. Zhang, R. Yang, P. Cieplak, R. Luo, T. Lee, J. Caldwell, J. M. Wang, P. Kollman, J. Comput. Chem. 2003, 24, 1999-2012.

J. M. Wang, R. M. Wolf, J. W. Caldwell, P. A. Kollman, D. A. Case, J. Comput. Chem. 2004, 25, 1157-1174.

O. Korb, T. Stutzle, T. E. Exner, J. Chem. Inf. Model. 2009, 49, 84-96.

O. Trott, A. J. Olson, J. Comput. Chem. 2010, 31, 455-461.

M. D. Eldridge, C. W. Murray, T. R. Auton, G. V. Paolini, R. P. Mee, J. Comput.-Aided Mol. Des. 1997, 11, 425-445.

G. Jones, P. Willett, R. C. Glen, A. R. Leach, R. Taylor, J. Mol. Biol. 1997, 267, 727-748.

W. T. M. Mooij, M. L. Verdonk, Proteins 2005, 61, 272-287.

G. M. Morris, R. Huey, W. Lindstrom, M. F. Sanner, R. K. Belew, D. S. Goodsell, A. J. Olson, J. Comput. Chem. 2009, 30, 2785-2791.

W. J. Allen, T. E. Balius, S. Mukherjee, S. R. Brozell, D. T. Moustakas, P. T. Lang, D. A. Case, I. D. Kuntz, R. C. Rizzo, J. Comput. Chem. 2015, 36, 1132-1156.

D. A. Pearlman, P. S. Charifson, J. Med. Chem. 2001, 44, 3417-3423.

M. M. Mysinger, M. Carchia, J. J. Irwin, B. K. Shoichet, J. Med. Chem. 2012, 55, 6582-6594.

D. R. Koes, M. P. Baumgartner, C. J. Camacho, J. Chem. Inf. Model. 2013, 53, 1893-1904.

A. Nicholls, J. Comput.-Aided Mol. Des. 2008, 22, 239-255.

M. De Vivo, A. Cavalli, Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2017, 7, e1320.

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