Virtual Screening of Telaprevir and Danoprevir Derivatives for Hepatitis C Virus NS3/4A Protease Inhibitors

Kaushik      Sarkar; Rajesh   Kumar   Das
doi:10.2174/1570180820666221207110739
Abstract

Background: The NS3/4A protease is a common target for inhibiting hepatitis C virus (HCV) infection. Telaprevir and danoprevir have promising activity in combating these virus-associated infections and are used as HCV protease inhibitors.
Objective: In this study, we have found different tested derivative compounds for developing various HCV NS3/4A protease inhibitors by designing the chemical structures of telaprevir and danoprevir.
Methods: In silico studies were carried out to find better drug candidatures from these derivative compounds. The docking studies were performed on HCV NS3/4A protease receptors (PDB: 3SV6 & 5EQR) using Autodock vina. DFT, global reactivity, ADME (Absorption, distribution, metabolism & excretion), and toxicity analysis were also performed for these designed compounds. The stability of the proteinligand complexes was quantified by MD simulation and MMPBSA studies.
Results: 16 derivatives (four as telaprevir and twelve as danoprevir) have satisfied higher binding affinity of interaction with NS3/4A protease, compared to telaprevir and danoprevir. These compounds have also passed all rules of drug candidature to serve as the best HCV inhibitors.
Conclusion: These 16 ligands can be effective inhibitors against HCV NS3/4A protease. These ligands must obey the drug candidate behavior by in vitro and in vivo analysis to inhibit HCV infection.
« Previous Next »
Graphical Abstract

[1]
Lavanchy, D. Evolving epidemiology of hepatitis C virus. Clin. Microbiol. Infect.,  2011, 17(2), 107-115.
 [http://dx.doi.org/10.1111/j.1469-0691.2010.03432.x] [PMID: 21091831]

[2]
Zakalashvili, M.; Zarkua, J.; Gish, R.G.; Zhamutashvili, M.; Sartania, V.; Weizenegger, M.; Bartel, J.; Raabe, M.; Gvinjilia, L.; Metreveli, S.; Barnova, M.; Abramishvili, N.; Rtskhiladze, I.; Metreveli, D. Assessment of treatment options for patients with hepatitis C virus recombinant form 2k/1b. Hepatol. Res.,  2021, 51(2), 156-165.
 [http://dx.doi.org/10.1111/hepr.13587] [PMID: 33207029]

[3]
Foster, G.R.; Irving, W.L.; Cheung, M.C.M.; Walker, A.J.; Hudson, B.E.; Verma, S.; McLauchlan, J.; Mutimer, D.J.; Brown, A.; Gelson, W.T.H.; MacDonald, D.C.; Agarwal, K. Impact of direct acting antiviral therapy in patients with chronic hepatitis C and decompensated cirrhosis. J. Hepatol.,  2016, 64(6), 1224-1231.
 [http://dx.doi.org/10.1016/j.jhep.2016.01.029] [PMID: 26829205]

[4]
Jiang, X.; Tan, J.; Wang, Y.; Chen, J.; Li, J.; Jiang, Z.; Quan, Y.; Jin, J.; Li, Y.; Cen, S.; Li, Y.; Peng, Z.; Li, Z. 2-((4-Arylpiperazin-1-yl)methyl)benzonitrile derivatives as orally available inhibitors of hepatitis C virus with a novel mechanism of action. J. Med. Chem.,  2020, 63(11), 5972-5989.
 [http://dx.doi.org/10.1021/acs.jmedchem.0c00232] [PMID: 32378892]

[5]
Li, G.; De Clercq, E. Current therapy for chronic hepatitis C: The role of direct-acting antivirals. Antiviral Res.,  2017, 142, 83-122.
 [http://dx.doi.org/10.1016/j.antiviral.2017.02.014] [PMID: 28238877]

[6]
Keating, G.M. Ledipasvir/Sofosbuvir: A review of its use in chronic hepatitis C. Drugs,  2015, 75(6), 675-685.
 [http://dx.doi.org/10.1007/s40265-015-0381-2] [PMID: 25837989]

[7]
Geddawy, A.; Ibrahim, Y.F.; Elbahie, N.M.; Ibrahim, M.A. Direct acting anti-hepatitis C virus drugs: Clinical pharmacology and future direction. J. Transl. Int. Med.,  2017, 5(1), 8-17.
 [http://dx.doi.org/10.1515/jtim-2017-0007] [PMID: 28680834]

[8]
Lawitz, E.J.; O’Riordan, W.D.; Asatryan, A.; Freilich, B.L.; Box, T.D.; Overcash, J.S.; Lovell, S.; Ng, T.I.; Liu, W.; Campbell, A.; Lin, C.W.; Yao, B.; Kort, J. Potent antiviral activities of the direct-acting antivirals ABT-493 and ABT-530 with three-day monotherapy for hepatitis C virus genotype 1 infection. Antimicrob. Agents Chemother.,  2016, 60(3), 1546-1555.
 [http://dx.doi.org/10.1128/AAC.02264-15] [PMID: 26711747]

[9]
Shiryaev, S.A.; Thomsen, E.R.; Cieplak, P.; Chudin, E.; Cheltsov, A.V.; Chee, M.S.; Kozlov, I.A.; Strongin, A.Y. New details of HCV NS3/4A proteinase functionality revealed by a high-throughput cleavage assay. PLoS One,  2012, 7(4), e35759.
 [http://dx.doi.org/10.1371/journal.pone.0035759] [PMID: 22558217]

[10]
Meewan, I.; Zhang, X.; Roy, S.; Ballatore, C.; O’Donoghue, A.J.; Schooley, R.T.; Abagyan, R. Discovery of new inhibitors of hepatitis C virus NS3/4A protease and its D168A mutant. ACS Omega,  2019, 4(16), 16999-17008.
 [http://dx.doi.org/10.1021/acsomega.9b02491] [PMID: 31646247]

[11]
Appleby, T.C.; Anderson, R.; Fedorova, O.; Pyle, A.M.; Wang, R.; Liu, X.; Brendza, K.M.; Somoza, J.R. Visualizing ATP-dependent RNA translocation by the NS3 helicase from HCV. J. Mol. Biol.,  2011, 405(5), 1139-1153.
 [http://dx.doi.org/10.1016/j.jmb.2010.11.034] [PMID: 21145896]

[12]
Love, R.A.; Parge, H.E.; Wickersham, J.A.; Hostomsky, Z.; Habuka, N.; Moomaw, E.W.; Adachi, T.; Hostomska, Z. The crystal structure of hepatitis C virus NS3 proteinase reveals a trypsin-like fold and a structural zinc binding site. Cell,  1996, 87(2), 331-342.
 [http://dx.doi.org/10.1016/S0092-8674(00)81350-1] [PMID: 8861916]

[13]
Yao, N.; Reichert, P.; Taremi, S.S.; Prosise, W.W.; Weber, P.C. Molecular views of viral polyprotein processing revealed by the crystal structure of the hepatitis C virus bifunctional protease–helicase. Structure,  1999, 7(11), 1353-1363.
 [http://dx.doi.org/10.1016/S0969-2126(00)80025-8] [PMID: 10574797]

[14]
Li, K.; Foy, E.; Ferreon, J.C.; Nakamura, M.; Ferreon, A.C.M.; Ikeda, M.; Ray, S.C.; Gale, M., Jr; Lemon, S.M. Immune evasion by hepatitis C virus NS3/4A protease-mediated cleavage of the Toll-like receptor 3 adaptor protein TRIF. Proc. Natl. Acad. Sci. USA,  2005, 102(8), 2992-2997.
 [http://dx.doi.org/10.1073/pnas.0408824102] [PMID: 15710891]

[15]
Kawai, T.; Takahashi, K.; Sato, S.; Coban, C.; Kumar, H.; Kato, H.; Ishii, K.J.; Takeuchi, O.; Akira, S. IPS-1, an adaptor triggering RIG-I- and Mda5-mediated type I interferon induction. Nat. Immunol.,  2005, 6(10), 981-988.
 [http://dx.doi.org/10.1038/ni1243] [PMID: 16127453]

[16]
Seth, R.B.; Sun, L.; Ea, C.K.; Chen, Z.J. Identification and characterization of MAVS, a mitochondrial antiviral signaling protein that activates NF-kappaB and IRF 3. Cell,  2005, 122(5), 669-682.
 [http://dx.doi.org/10.1016/j.cell.2005.08.012] [PMID: 16125763]

[17]
Soumana, D.I.; Kurt Yilmaz, N.; Ali, A.; Prachanronarong, K.L.; Schiffer, C.A. Molecular and dynamic mechanism underlying drug resistance in genotype 3 hepatitis C NS3/4A protease. J. Am. Chem. Soc.,  2016, 138(36), 11850-11859.
 [http://dx.doi.org/10.1021/jacs.6b06454] [PMID: 27512818]

[18]
De Clercq, E. Development of antiviral drugs for the treatment of hepatitis C at an accelerating pace. Rev. Med. Virol.,  2015, 25(4), 254-267.
 [http://dx.doi.org/10.1002/rmv.1842] [PMID: 26043288]

[19]
De Clercq, E.; Li, G. Approved antiviral drugs over the past 50 years. Clin. Microbiol. Rev.,  2016, 29(3), 695-747.
 [http://dx.doi.org/10.1128/CMR.00102-15] [PMID: 27281742]

[20]
De Clercq, E. C-nucleosides to be revisited. J. Med. Chem.,  2016, 59(6), 2301-2311.
 [http://dx.doi.org/10.1021/acs.jmedchem.5b01157] [PMID: 26513594]

[21]
De Clercq, E. Current race in the development of DAAs (direct-acting antivirals) against HCV. Biochem. Pharmacol.,  2014, 89(4), 441-452.
 [http://dx.doi.org/10.1016/j.bcp.2014.04.005] [PMID: 24735613]

[22]
Rivero-Juarez, A.; Brieva, T.; Frias, M.; Rivero, A. Pharmacodynamic and pharmacokinetic evaluation of the combination of daclatasvir/sofosbuvir/ribavirin in the treatment of chronic hepatitis C. Expert Opin. Drug Metab. Toxicol.,  2018, 14(9), 901-910.
 [http://dx.doi.org/10.1080/17425255.2018.1506765] [PMID: 30058394]

[23]
Cotter, T.G.; Jensen, D.M. Glecaprevir/pibrentasvir for the treatment of chronic hepatitis C: design, development, and place in therapy. Drug Des. Devel. Ther.,  2019, 13, 2565-2577.
 [http://dx.doi.org/10.2147/DDDT.S172512] [PMID: 31534310]

[24]
Carrat, F.; Fontaine, H.; Dorival, C.; Simony, M.; Diallo, A.; Hezode, C.; De Ledinghen, V.; Larrey, D.; Haour, G.; Bronowicki, J.P.; Zoulim, F.; Asselah, T.; Marcellin, P.; Thabut, D.; Leroy, V.; Tran, A.; Habersetzer, F.; Samuel, D.; Guyader, D.; Chazouilleres, O.; Mathurin, P.; Metivier, S.; Alric, L.; Riachi, G.; Gournay, J.; Abergel, A.; Cales, P.; Ganne, N.; Loustaud-Ratti, V.; D’Alteroche, L.; Causse, X.; Geist, C.; Minello, A.; Rosa, I.; Gelu-Simeon, M.; Portal, I.; Raffi, F.; Bourliere, M.; Pol, S. Clinical outcomes in patients with chronic hepatitis C after direct-acting antiviral treatment: A prospective cohort study. Lancet,  2019, 393(10179), 1453-1464.
 [http://dx.doi.org/10.1016/S0140-6736(18)32111-1] [PMID: 30765123]

[25]
Das, D.; Pandya, M. Recent advancement of direct-acting antiviral agents (DAAs) in hepatitis C therapy. Mini Rev. Med. Chem.,  2018, 18(7), 584-596.
 [http://dx.doi.org/10.2174/1389557517666170913111930] [PMID: 28901852]

[26]
Ellis, S. Chinese approval for Ascletis’ HCV drug is first homegrown success. Nat. Biotechnol.,  2018, 36(8), 675-676.
 [http://dx.doi.org/10.1038/nbt0818-675a] [PMID: 30080821]

[27]
Miao, M.; Jing, X.; De Clercq, E.; Li, G. Danoprevir for the treatment of hepatitis c virus infection: design, development, and place in therapy. Drug Des. Devel. Ther.,  2020, 14, 2759-2774.
 [http://dx.doi.org/10.2147/DDDT.S254754] [PMID: 32764876]

[28]
Mitruka, K.; Tsertsvadze, T.; Butsashvili, M.; Gamkrelidze, A.; Sabelashvili, P.; Adamia, E.; Chokheli, M.; Drobeniuc, J.; Hagan, L.; Harris, A.M.; Jiqia, T.; Kasradze, A.; Ko, S.; Qerashvili, V.; Sharvadze, L.; Tskhomelidze, I.; Kvaratskhelia, V.; Morgan, J.; Ward, J.W.; Averhoff, F. Launch of a nationwide hepatitis C elimination program-Georgia, April 2015. MMWR Morb. Mortal. Wkly. Rep.,  2015, 64(28), 753-757.
 [http://dx.doi.org/10.15585/mmwr.mm6428a2] [PMID: 26203628]

[29]
Rosenquist, Å.; Samuelsson, B.; Johansson, P.O.; Cummings, M.D.; Lenz, O.; Raboisson, P.; Simmen, K.; Vendeville, S.; de Kock, H.; Nilsson, M.; Horvath, A.; Kalmeijer, R.; de la Rosa, G.; Beumont-Mauviel, M. Discovery and development of simeprevir (TMC435), a HCV NS3/4A protease inhibitor. J. Med. Chem.,  2014, 57(5), 1673-1693.
 [http://dx.doi.org/10.1021/jm401507s] [PMID: 24446688]

[30]
Belema, M.; Meanwell, N.A. Discovery of daclatasvir, a pan-genotypic hepatitis C virus NS5A replication complex inhibitor with potent clinical effect. J. Med. Chem.,  2014, 57(12), 5057-5071.
 [http://dx.doi.org/10.1021/jm500335h] [PMID: 24749835]

[31]
Sofia, M.J.; Bao, D.; Chang, W.; Du, J.; Nagarathnam, D.; Rachakonda, S.; Reddy, P.G.; Ross, B.S.; Wang, P.; Zhang, H.R.; Bansal, S.; Espiritu, C.; Keilman, M.; Lam, A.M.; Steuer, H.M.M.; Niu, C.; Otto, M.J.; Furman, P.A. Discovery of a β-d-2′-deoxy-2′-α-fluoro-2′-β-C-methyluridine nucleotide prodrug (PSI-7977) for the treatment of hepatitis C virus. J. Med. Chem.,  2010, 53(19), 7202-7218.
 [http://dx.doi.org/10.1021/jm100863x] [PMID: 20845908]

[32]
Smolders, E.J.; Jansen, A.M.E.; ter Horst, P.G.J.; Rockstroh, J.; Back, D.J.; Burger, D.M.; Viral Hepatitis, C. Viral hepatitis C therapy: Pharmacokinetic and pharmacodynamic considerations: A 2019 update. Clin. Pharmacokinet.,  2019, 58(10), 1237-1263.
 [http://dx.doi.org/10.1007/s40262-019-00774-0] [PMID: 31114957]

[33]
Goel, A.; Chen, Q.; Chhatwal, J.; Aggarwal, R. Cost‐effectiveness of generic pan‐genotypic sofosbuvir/velpatasvir versus genotype‐dependent direct‐acting antivirals for hepatitis C treatment. J. Gastroenterol. Hepatol.,  2018, 33(12), 2029-2036.
 [http://dx.doi.org/10.1111/jgh.14301] [PMID: 29864213]

[34]
Martinello, M.; Orkin, C.; Cooke, G.; Bhagani, S.; Gane, E.; Kulasegaram, R.; Shaw, D.; Tu, E.; Petoumenos, K.; Marks, P.; Grebely, J.; Dore, G.J.; Nelson, M.; Matthews, G.V. Short‐duration pan‐genotypic therapy with glecaprevir/pibrentasvir for 6 weeks among people with recent hepatitis C viral infection. Hepatology,  2020, 72(1), 7-18.
 [http://dx.doi.org/10.1002/hep.31003] [PMID: 31652357]

[35]
Bourlière, M.; Gordon, S.C.; Flamm, S.L.; Cooper, C.L.; Ramji, A.; Tong, M.; Ravendhran, N.; Vierling, J.M.; Tran, T.T.; Pianko, S.; Bansal, M.B.; de Lédinghen, V.; Hyland, R.H.; Stamm, L.M.; Dvory-Sobol, H.; Svarovskaia, E.; Zhang, J.; Huang, K.C.; Subramanian, G.M.; Brainard, D.M.; McHutchison, J.G.; Verna, E.C.; Buggisch, P.; Landis, C.S.; Younes, Z.H.; Curry, M.P.; Strasser, S.I.; Schiff, E.R.; Reddy, K.R.; Manns, M.P.; Kowdley, K.V.; Zeuzem, S. Sofosbuvir, Velpatasvir, and Voxilaprevir for previously treated HCV infection. N. Engl. J. Med.,  2017, 376(22), 2134-2146.
 [http://dx.doi.org/10.1056/NEJMoa1613512] [PMID: 28564569]

[36]
Cox, A.L. Challenges and promise of a hepatitis C virus vaccine. Cold Spring Harb. Perspect. Med.,  2020, 10(2), a036947.
 [http://dx.doi.org/10.1101/cshperspect.a036947] [PMID: 31548228]

[37]
Lok, A.S.; Sulkowski, M.S.; Kort, J.J.; Willner, I.; Reddy, K.R.; Shiffman, M.L.; Hassan, M.A.; Pearlman, B.L.; Hinestrosa, F.; Jacobson, I.M.; Morelli, G.; Peter, J.A.; Vainorius, M.; Michael, L.C.; Fried, M.W.; Wang, G.P.; Lu, W.; Larsen, L.; Nelson, D.R. Efficacy of glecaprevir and pibrentasvir in patients with genotype 1 hepatitis c virus infection with treatment failure after NS5A inhibitor plus sofosbuvir therapy. Gastroenterology,  2019, 157(6), 1506-1517.e1.
 [http://dx.doi.org/10.1053/j.gastro.2019.08.008] [PMID: 31401140]

[38]
Li, D.K.; Chung, R.T. Overview of direct-acting antiviral drugs and drug resistance of hepatitis C virus. Methods Mol. Biol.,  2019, 8976-8978.
 [http://dx.doi.org/10.1007/978-1-4939-8976-8_1]

[39]
Hajarizadeh, B.; Grebely, J.; Martinello, M.; Matthews, G.V.; Lloyd, A.R.; Dore, G.J. Hepatitis C treatment as prevention: Evidence, feasibility, and challenges. Lancet Gastroenterol. Hepatol.,  2016, 1(4), 317-327.
 [http://dx.doi.org/10.1016/S2468-1253(16)30075-9] [PMID: 28404202]

[40]
Romano, K.P.; Ali, A.; Aydin, C.; Soumana, D.; Özen, A.; Deveau, L.M.; Silver, C.; Cao, H.; Newton, A.; Petropoulos, C.J.; Huang, W.; Schiffer, C.A. The molecular basis of drug resistance against hepatitis C virus NS3/4A protease inhibitors. PLoS Pathog.,  2012, 8(7), e1002832.
 [http://dx.doi.org/10.1371/journal.ppat.1002832] [PMID: 22910833]

[41]
Matthews, S.J.; Lancaster, J.W. Telaprevir: A hepatitis C NS3/4A protease inhibitor. Clin. Ther.,  2012, 34(9), 1857-1882.
 [http://dx.doi.org/10.1016/j.clinthera.2012.07.011] [PMID: 22951253]

[42]
Markham, A.; Keam, S.J. Danoprevir: First global approval. Drugs,  2018, 78(12), 1271-1276.
 [http://dx.doi.org/10.1007/s40265-018-0960-0] [PMID: 30117020]

[43]
Chen, H.; Zhang, Z.; Wang, L.; Huang, Z.; Gong, F.; Li, X.; Chen, Y.; Wu, J.J. First clinical study using HCV protease inhibitor danoprevir to treat COVID-19 patients. Medicine (Baltimore),  2020, 99(48), e23357.
 [http://dx.doi.org/10.1097/MD.0000000000023357] [PMID: 33235105]

[44]
Hanwell, M.D.; Curtis, D.E.; Lonie, D.C.; Vandermeersch, T.; Zurek, E.; Hutchison, G.R. Avogadro: an advanced semantic chemical editor, visualization, and analysis platform. J. Cheminform.,  2012, 4(1), 17.
 [http://dx.doi.org/10.1186/1758-2946-4-17] [PMID: 22889332]

[45]
Parr, R.G.; Yang, W. Density functional theory of atoms and molecules. Oxford University Press,  1989, 1, 989.

[46]
Dreizler, R.M.; da Providência, J. Density functional methods in physics; Springer Science & Business Media: New York, 2013. 

[47]
Frisch, M.J.T.; Schlegel, H.B.; Scuseria, G.E.; Robb, M.A.; Cheeseman, J.R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G.A.; Nakatsuji, H.; Caricato, M.; Li, X.; Hratchian, H.P.; Izmaylov, A.F.; Bloino, J.; Zheng, G.; Sonnenberg, J.L.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Vreven, T.; Montgomery, J.A. Jr.; Peralta, J.E.; Ogliaro, F.; Bearpark, M.; Heyd, J.J.; Brothers, E.; Kudin, K.N.; Staroverov, V.N.; Kobayashi, R.; Normand, J.; Raghavachari, K.; Rendell, A.; Burant, J.C.; Iyengar, S.S.; Tomasi, J.; Cossi, M.; Rega, N.; Millam, J.M.; Klene, M.; Knox, J.E.; Cross, J.B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R.E.; Yazyev, O.; Austin, A.J.; Cammi, R.; Pomelli, C.; Ochterski, J.W.; Martin, R.L.; Morokuma, K.; Zakrzewski, V.G.; Voth, G.A.; Salvador, P.; Dannenberg, J.J.; Dapprich, S.; Daniels, A.D.; Farkas, Ö.; Foresman, J.B.; Ortiz, J.V.; Cioslowski, J.; Fox, D.J. Gaussian 09, Revision E.01; Gaussian, Inc.: Wallingford, CT, 2009. 

[48]
Stephens, P.J.; Devlin, F.J.; Chabalowski, C.F.; Frisch, M.J. Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields. J. Phys. Chem.,  1994, 98(45), 11623-11627.
 [http://dx.doi.org/10.1021/j100096a001]

[49]
Lee, C.; Yang, W.; Parr, R.G. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys. Rev. B Condens. Matter,  1988, 37(2), 785-789.
 [http://dx.doi.org/10.1103/PhysRevB.37.785] [PMID: 9944570]

[50]
Trott, O.; Olson, A.J. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem.,  2010, 31(2), 455-461.
 [PMID: 19499576]

[51]
Lee, S.; Tran, A.; Allsopp, M.; Lim, J.B.; Hénin, J.; Klauda, J.B. CHARMM36 united atom chain model for lipids and surfactants. J. Phys. Chem. B,  2014, 118(2), 547-556.
 [http://dx.doi.org/10.1021/jp410344g] [PMID: 24341749]

[52]
Boonstra, S.; Onck, P.R.; van der Giessen, E. CHARMM TIP3P water model suppresses peptide folding by solvating the unfolded state. J. Phys. Chem. B,  2016, 120(15), 3692-3698.
 [http://dx.doi.org/10.1021/acs.jpcb.6b01316] [PMID: 27031562]

[53]
Vanommeslaeghe, K.; Hatcher, E.; Acharya, C.; Kundu, S.; Zhong, S.; Shim, J.; Darian, E.; Guvench, O.; Lopes, P.; Vorobyov, I.; Mackerell, A.D. Jr. CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J. Comput. Chem.,  2010, 31(4), 671-690.
 [PMID: 19575467]

[54]
Vanommeslaeghe, K.; MacKerell, A.D., Jr Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing. J. Chem. Inf. Model.,  2012, 52(12), 3144-3154.
 [http://dx.doi.org/10.1021/ci300363c] [PMID: 23146088]

[55]
Abraham, M.J.; Gready, J.E. Optimization of parameters for molecular dynamics simulation using smooth particle-mesh Ewald in GROMACS 4.5. J. Comput. Chem.,  2011, 32(9), 2031-2040.
 [http://dx.doi.org/10.1002/jcc.21773] [PMID: 21469158]

[56]
Kumari, R.; Kumar, R.; Lynn, A.; Lynn, A. g_mmpbsa--a GROMACS tool for high-throughput MM-PBSA calculations. J. Chem. Inf. Model.,  2014, 54(7), 1951-1962.
 [http://dx.doi.org/10.1021/ci500020m] [PMID: 24850022]

[57]
Baker, N.A.; Sept, D.; Joseph, S.; Holst, M.J.; McCammon, J.A. Electrostatics of nanosystems: Application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA,  2001, 98(18), 10037-10041.
 [http://dx.doi.org/10.1073/pnas.181342398] [PMID: 11517324]

[58]
Kollman, P.A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.J.A.o.c.r. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc. Chem. Res.,  2000, 33(12), 889-897.
 [http://dx.doi.org/10.1021/ar000033j]

[59]
Narkhede, R.R.; Cheke, R.S.; Ambhore, J.P. SHİNDE, S. The molecular docking study of potential drug candidates showing anti-COVID-19 activity by exploring of therapeutic targets of SARS-CoV-2. Eur. J. Med. Oncol.,  2020, 4(3), 185-195.

[60]
Rastogi, S.; Rastogi, P.; Mendiratta, N. Bioinformatics Methods and Applications: Genomics Proteomics And Drug Discovery, 3rd ed; PHI Learning Pvt. Ltd.: Delhi, 2008. 

[61]
Rahman, M.A.; Chakma, U.; Kumer, A.; Rahman, M.R.; Matin, M.M. Uridine-derived 4-Aminophenyl 1-Thioglucosides: DFT optimized FMO, ADME, and antiviral activities study. Biointerface Res. Appl. Chem.,  2023, 13(1), 1-15.

[62]
Oyedele, A-Q.K.; Ogunlana, A.T.; Boyenle, I.D.; Adeyemi, A.O.; Rita, T.O.; Adelusi, T.I.; Abdul-Hammed, M.; Elegbeleye, O.E.; Odunitan, T.T.J.M.D. Docking covalent targets for drug discovery: Stimulating the computer-aided drug design community of possible pitfalls and erroneous practices. Mol. Divers.,  2022, 1-25.
 [http://dx.doi.org/10.1007/s11030-022-10523-4]

[63]
Sarkar, K.; Sarkar, S.; Das, R.K. Screening of drug efficacy of Rosmarinic Acid derivatives as Aurora kinase inhibitors by computer aided drug design method. Curr. Comput. Aided Drug Des.,  2020, 3(10), 1573409916666200703170045.
 [PMID: 32619178]

[64]
Umar, Y.; Abdalla, S. DFT study of the molecular structure, conformational preference, HOMO, LUMO, and vibrational analysis of 2-, and 3-furoyl chloride. J. Solution Chem.,  2017, 46(4), 741-758.
 [http://dx.doi.org/10.1007/s10953-017-0601-3]

[65]
Sarkar, K.; Das, R.K. In silico study of rosmarinic acid derivatives as novel insulin fibril inhibitors. J. Comput. Biophys. Chem.,  2021, 20(6), 641-654.
 [http://dx.doi.org/10.1142/S2737416521500381]

[66]
Reed, J.L. Electronegativity: Chemical hardness I. J. Phys. Chem. A,  1997, 101(40), 7396-7400.
 [http://dx.doi.org/10.1021/jp9711050]

[67]
Arjunan, V.; Devi, L.; Subbalakshmi, R.; Rani, T.; Mohan, S. Synthesis, vibrational, NMR, quantum chemical and structure-activity relation studies of 2-hydroxy-4-methoxyacetophenone. Spectrochim. Acta A Mol. Biomol. Spectrosc.,  2014, 130, 164-177.
 [http://dx.doi.org/10.1016/j.saa.2014.03.121] [PMID: 24792193]

[68]
El-Gammal, O.A.; Rakha, T.H.; Metwally, H.M.; Abu El-Reash, G.M. Synthesis, characterization, DFT and biological studies of isatinpicolinohydrazone and its Zn(II), Cd(II) and Hg(II) complexes. Spectrochim. Acta A Mol. Biomol. Spectrosc.,  2014, 127, 144-156.
 [http://dx.doi.org/10.1016/j.saa.2014.02.008] [PMID: 24632168]

[69]
Parr, R.G.; Yang, W. Density functional approach to the frontier-electron theory of chemical reactivity. J. Am. Chem. Soc.,  1984, 106(14), 4049-4050.
 [http://dx.doi.org/10.1021/ja00326a036]

[70]
Pitzer, K.S. The nature of the chemical bond and the structure of molecules and crystals: An introduction to modern structural chemistry. J. Am. Chem. Soc.,  1960, 82(15), 4121-4121.
 [http://dx.doi.org/10.1021/ja01500a088]

[71]
Lipinski, C.A.; Lombardo, F.; Dominy, B.W.; Feeney, P.J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Deliv. Rev.,  2012, 64, 4-17.

[72]
Husain, A.; Ahmad, A.; Khan, S.A.; Asif, M.; Bhutani, R.; Al-Abbasi, F.A. Synthesis, molecular properties, toxicity and biological evaluation of some new substituted imidazolidine derivatives in search of potent anti-inflammatory agents. Saudi Pharm. J.,  2016, 24(1), 104-114.
 [http://dx.doi.org/10.1016/j.jsps.2015.02.008] [PMID: 26903774]

[73]
Lee, S.; Lee, I.; Kim, H.; Chang, G.; Chung, J.; No, K. The PreADME Approach: Web-based Program for Rapid Prediction of Physico-chemical, Drug Absorption and Drug-like Properties. In: EuroQSAR designing drugs and crop protectants: processes, problems and solutions; Blackwell Science Inc.: Hoboken, 2003; pp. 418-420.
Rights & Permissions Print Cite
Explore Articles
Open Access
Open Access Articles
DOI https://dx.doi.org/10.2174/1570180820666221207110739	Print ISSN 1570-1808
Publisher Name Bentham Science Publisher	Online ISSN 1875-628X
Letters in Drug Design & Discovery

Virtual Screening of Telaprevir and Danoprevir Derivatives for Hepatitis C Virus NS3/4A Protease Inhibitors

Abstract Play Pause

Graphical Abstract

Abstract
