358
Views
1
CrossRef citations to date
0
Altmetric
Research Article

E-pharmacophore based screening to identify potential HIV-1 gp120 and CD4 interaction blockers for wild and mutant types

, , &
Pages 353-377 | Received 23 Nov 2020, Accepted 07 Mar 2021, Published online: 09 Apr 2021

References

  • Global HIV & AIDS statistics — 2020 fact sheet | UNAIDS, Available at https://www.unaids.org/en/resources/fact-sheet (Accessed Feb 18, 2020).
  • J.M. Lalonde, M.A. Elban, J.R. Courter, A. Sugawara, T. Soeta, N. Madani, A.M. Princiotto, Y.D. Kwon, P.D. Kwong, A. Schön, E. Freire, J. Sodroski, and A.B. Smith III, Design, synthesis and biological evaluation of small molecule inhibitors of CD4-gp120 binding based on virtual screening, Bioorg. Med. Chem. 19 (2011), pp. 91–101. doi:10.1016/j.bmc.2010.11.049.
  • R.W. Shafer and D.A. Vuitton, Highly active antiretroviral therapy (HAART) for the treatment of infection with human immunodeficiency virus type 1, Biomed. Pharmacother. 53 (1999), pp. 73–86. doi:10.1016/S0753-3322(99)80063-8.
  • R.J. Lu, J.A. Tucker, T. Zinevitch, O. Kirichenko, V. Konoplev, S. Kuznetsova, S. Sviridov, J. Pickens, S. Tandel, E. Brahmachary, Y. Yang, J. Wang, S. Freel, S. Fisher, A. Sullivan, J. Zhou, S. Stanfield-Oakley, M. Greenberg, D. Bolognesi, B. Bray, B. Koszalka, P. Jeffs, A. Khasanov, Y.A. Ma, C. Jeffries, C. Liu, T. Proskurina, T. Zhu, A. Chucholowski, R. Li, and C. Sexton, Design and synthesis of human immunodeficiency virus entry inhibitors: Sulfonamide as an isostere for the α-ketoamide group, J. Med. Chem. 50 (2007), pp. 6535–6544. doi:10.1021/jm070650e.
  • F. Curreli, Y.D. Kwon, D.S. Belov, R.R. Ramesh, A.V. Kurkin, A. Altieri, P.D. Kwong, and A.K. Debnath, Synthesis, antiviral potency, in vitro ADMET, and X-ray structure of potent CD4 mimics as entry inhibitors that target the Phe43 cavity of HIV-1 gp120, J. Med. Chem. 60 (2017), pp. 3124–3153. doi:10.1021/acs.jmedchem.7b00179.
  • J.T. Leonard and K. Roy, The HIV entry inhibitors revisited, Curr. Med. Chem. 13 (2006), pp. 911–934. doi:10.2174/092986706776361030.
  • V. Briz, E. Poveda, and V. Soriano, HIV entry inhibitors: Mechanisms of action and resistance pathways, J. Antimirob. Chemother. 57 (2006), pp. 619–627. doi:10.1093/jac/dkl027.
  • P. Acharya, S. Lusvarghi, C.A. Bewley, and P.D. Kwong, HIV-1 gp120 as a therapeutic target: Navigating a moving labyrinth, Expert Opin. Ther. Targets 19 (2015), pp. 765–783. doi:10.1517/14728222.2015.1010513.
  • K. Vermeire and D. Schols, Anti-HIV agents targeting the interaction of gp120 with the cellular CD4 receptor, Expert Opin. Investig. Drugs 14 (2005), pp. 1199–1212. doi:10.1517/13543784.14.10.1199.
  • P.D. Kwong, R. Wyatt, J. Robinson, R.W. Sweet, J. Sodroski, and W.A. Hendrickson, Structure of an HIV gp 120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody, Nature 393 (1998), pp. 648–659. doi:10.1038/31405.
  • N. Madani, A. Schön, A.M. Princiotto, J.M. Lalonde, J.R. Courter, T. Soeta, D. Ng, L. Wang, E.T. Brower, S.H. Xiang, Y.D. Kwon, C.C. Huang, R. Wyatt, P.D. Kwong, E. Freire, A.B. Smith III, and J. Sodroski, Small-molecule CD4 mimics interact with a highly conserved pocket on HIV-1 gp120, Structure 16 (2008), pp. 1689–1701. doi:10.1016/j.str.2008.09.005.
  • J.R. Courter, N. Madani, J. Sodroski, A. Schön, E. Freire, P.D. Kwong, W.A. Hendrickson, I.M. Chaiken, J.M. Lalonde, and A.B. Smith III, Structure-based design, synthesis and validation of CD4-mimetic small molecule inhibitors of HIV-1 entry: Conversion of a viral entry agonist to an antagonist, Acc. Chem. Res. 47 (2014), pp. 1228–1237. doi:10.1021/ar4002735.
  • A.M. Andrianov, I.A. Kashyn, and A.V. Tuzikov, Computational identification of novel entry inhibitor scaffolds mimicking primary receptor CD4 of HIV-1 gp120, J. Mol. Model. 23 (2017), pp. 18. doi:10.1007/s00894-016-3189-4.
  • F. Curreli, D.S. Belov, Y.D. Kwon, R. Ramesh, A.M. Furimsky, K. O’Loughlin, P.C. Byrge, L.V. Iyer, J.C. Mirsalis, A.V. Kurkin, A. Altieri, and A.K. Debnath, Structure-based lead optimization to improve antiviral potency and ADMET properties of phenyl-1H-pyrrole-carboxamide entry inhibitors targeted to HIV-1 gp120, Eur. J. Med. Chem. 154 (2018), pp. 367–391. doi:10.1016/j.ejmech.2018.04.062.
  • W. Li, L. Lu, W. Li, and S. Jiang, Small-molecule HIV-1 entry inhibitors targeting gp120 and gp41: A patent review (2010–2015), Expert Opin. Ther. Pat. 27 (2017), pp. 707–719. doi:10.1080/13543776.2017.1281249.
  • E.V. Rullo, M. Ceccarelli, F. Condorelli, A. Facciolà, G. Visalli, F. D’Aleo, I. Paolucci, B. Cacopardo, M.R. Pinzone, M.D. Rosa, G. Nunnari, and G.F. Pellicanò, Investigational drugs in HIV: Pros and cons of entry and fusion inhibitors (review), Mol. Med. Rep. 19 (2019), pp. 1987–1995. doi:10.3892/mmr.2019.9840.
  • U. Panwar, I. Chandra, C. Selvaraj, and S.K. Singh, Current computational approaches for the development of anti-HIV inhibitors: An overview, Curr. Pharm. Des. 25 (2019), pp. 3390–3405. doi:10.2174/1381612825666190911160244.
  • Y.D. Kwon, J.M. LaLonde, Y. Yang, M.A. Elban, A. Sugawara, J.R. Courter, D.M. Jones, A.B. Smith III, A.K. Debnath, and P.D. Kwong, Crystal structures of HIV-1 gp120 envelope glycoprotein in complex with NBD analogues that target the CD4-binding site, PloS One 9 (2014), pp. e85940. doi:10.1371/journal.pone.0085940.
  • C.B. Wilen, J.C. Tilton, and R.W. Doms, HIV: Cell binding and entry, Cold Spring Harb. Perspect. Med. 2 (2012), pp. a006866. doi:10.1101/cshperspect.a006866.
  • B. Melillo, S. Liang, J. Park, A. Schön, J.R. Courter, J.M. Lalonde, D.J. Wendler, A.M. Princiotto, M.S. Seaman, E. Freire, J. Sodroski, N. Madani, W.A. Hendrickson, and A.B. Smith III, Small-molecule CD4-mimics: Structure-based optimization of HIV-1 entry inhibition, ACS Med. Chem. Lett. 7 (2016), pp. 330–334. doi:10.1021/acsmedchemlett.5b00471.
  • C. Godfrey, M.C. Thigpen, K.W. Crawford, P. Jean-Phillippe, D. Pillay, D. Persaud, D.R. Kuritzkes, M. Wainberg, E. Raizes, and J. Fitzgibbon, Global HIV antiretroviral drug resistance: A perspective and report of a national institute of allergy and infectious diseases consultation, J. Infect Dis. 216 (2017), pp. S798–S800. doi:10.1093/infdis/jix137.
  • C. Nayak, I. Chandra, and S.K. Singh, An in silico pharmacological approach toward the discovery of potent inhibitors to combat drug resistance HIV-1 protease variants, J. Cell. Biochem. 120 (2019), pp. 9063–9081. doi:10.1002/jcb.28181.
  • B. Lin, X. Sun, S. Su, C. Lv, X. Zhang, L. Lin, R. Wang, J. Fu, and D. Kang, HIV drug resistance in HIV positive individuals under antiretroviral treatment in Shandong Province, China, PloS One 12 (2017), pp. e0181997. doi:10.1371/journal.pone.0181997.
  • L. Menendez-Arias and J.A. Este, HIV-Resistance to viral entry inhibitors, Curr. Pharm. Des. 10 (2005), pp. 1845–1860. doi:10.2174/1381612043384574.
  • Q. Guo, H.T. Ho, I. Dicker, L. Fan, N. Zhou, J. Friborg, T. Wang, B.V. McAuliffe, H.G.H. Wang, R.E. Rose, H. Fang, H.T. Scarnati, D.R. Langley, N.A. Meanwell, R. Abraham, R.J. Colonno, and P.F. Lin, Biochemical and genetic characterizations of a novel human immunodeficiency virus type 1 inhibitor that blocks gp120-CD4 interactions, J. Virol. 77 (2003), pp. 10528–10536. doi:10.1128/jvi.77.19.10528-10536.2003.
  • M. Pancera, Y.T. Lai, T. Bylund, A. Druz, S. Narpala, S. O’Dell, A. Schön, R.T. Bailer, G.Y. Chuang, H. Geng, M.K. Louder, R. Rawi, D.I. Soumana, A. Finzi, A. Herschhorn, N. Madani, J. Sodroski, E. Freire, D.R. Langley, J.R. Mascola, A.B. McDermott, and P.D. Kwong, Crystal structures of trimeric HIV envelope with entry inhibitors BMS-378806 and BMS-626529, Nat. Chem. Biol. 13 (2017), pp. 1115–1122. doi:10.1038/nchembio.2460.
  • A. Herschhorn, C. Gu, F. Moraca, X. Ma, M. Farrell, A.B. Smith III, M. Pancera, P.D. Kwong, A. Schön, E. Freire, C. Abrams, S.C. Blanchard, W. Mothes, and J.G. Sodroski, The β20-β21 of gp120 Is a regulatory switch for HIV-1 Env conformational transitions, Nat. Commun. 8 (2017), pp. 1–12. doi:10.1038/s41467-017-01119-w.
  • Schrödinger Release 2020-1: Protein Preparation Wizard; Epik, Schrödinger, LLC, New York, NY, 2020; Impact, Schrödinger, LLC, New York, NY; Prime, Schrödinger, LLC, New York, NY, 2020.
  • K. Sharma, K. Patidar, M.A. Ali, P. Patil, H. Goud, T. Hussain, A. Nayarisseri, and S.K. Singh, Structure-based virtual screening for the identification of high affinity compounds as potent VEGFR2 inhibitors for the treatment of renal cell carcinoma, Curr. Top. Med. Chem. 18 (2018), pp. 2174–2185. doi:10.2174/1568026619666181130142237.
  • S. Abdel-Azeim, Revisiting OPLS-AA force field for the simulation of anionic surfactants in concentrated electrolyte solutions, J. Chem. Theory Comput. 16 (2020), pp. 1136–1145. doi:10.1021/acs.jctc.9b00947.
  • J.H. McAliley and D.A. Bruce, Development of force field parameters for molecular simulation of polylactide, J. Chem. Theory Comput. 7 (2011), pp. 3756–3767. doi:10.1021/ct200251x.
  • G.M. Sastry, M. Adzhigirey, T. Day, R. Annabhimoju, and W. Sherman, Protein and ligand preparation: Parameters, protocols, and influence on virtual screening enrichments, J. Comput. Aided Mol. Des. 27 (2013), pp. 221–234. doi:10.1007/s10822-013-9644-8.
  • D. Shivakumar, J. Williams, Y. Wu, W. Damm, J. Shelley, and W. Sherman, Prediction of absolute solvation free energies using molecular dynamics free energy perturbation and the OPLS force field, J. Chem. Theory Comput. 6 (2010), pp. 1509–1519. doi:10.1021/ct900587b.
  • G.A. Kaminski, R.A. Friesner, J. Tirado-Rives, and W.L. Jorgensen, Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides, J. Phys. Chem. B. 105 (2001), pp. 6474–6487. doi:10.1021/jp003919d.
  • S.K. Tripathi, C. Selvaraj, S.K. Singh, and K.K. Reddy, Molecular docking, QPLD, and ADME prediction studies on HIV-1 integrase leads, Med. Chem. Res. 21 (2012), pp. 4239–4251. doi:10.1007/s00044-011-9940-6.
  • Schrödinger Release 2020-1: Glide, Schrödinger, LLC, New York, NY, 2020.
  • R.A. Friesner, J.L. Banks, R.B. Murphy, T.A. Halgren, J.J. Klicic, D.T. Mainz, M.P. Repasky, E.H. Knoll, M. Shelley, J.K. Perry, D.E. Shaw, P. Francis, and P.S. Shenkin, Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy, J. Med. Chem. 47 (2004), pp. 1739–1749. doi:10.1021/jm0306430.
  • Schrödinger Release  2020-1: Phase, Schrödinger, LLC, New York, NY, 2020.
  • S.L. Dixon, A.M. Smondyrev, and S.N. Rao, PHASE: A novel approach to pharmacophore modeling and 3D database searching, Chem. Biol. Drug Des. 67 (2006), pp. 370–372. doi:10.1111/j.1747-0285.2006.00384.x.
  • K.K. Reddy and S.K. Singh, Combined ligand and structure-based approaches on HIV-1 integrase strand transfer inhibitors, Chem. Biol. Interact. 218 (2014), pp. 71–81. doi:10.1016/j.cbi.2014.04.011.
  • H. Kubinyi, Chemical similarity and biological activities, J. Braz. Chem. Soc. 13 (2002), pp. 717–726. doi:10.1590/S0103-50532002000600002.
  • K. Loving, N.K. Salam, and W. Sherman, Energetic analysis of fragment docking and application to structure-based pharmacophore hypothesis generation, J. Comput. Aided Mol. Des. 23 (2009), pp. 541–554. doi:10.1007/s10822-009-9268-1.
  • I. Chandra, A.K. Behera, and S.S. Cherian, Identification of potential inhibitors against the human influenza A virus targeting the CPSF30 and RNA binding domains of the NS1 protein: An e-pharmacophore approach, Indian J. Pharm. Educ. Res. 51 (2017), pp. 25–33. doi:10.5530/ijper.51.1.5.
  • P.J. Therese, D. Manvar, S. Kondepudi, M.B. Battu, D. Sriram, A. Basu, P. Yogeeswari, and N. Kaushik-Basu, Multiple e-pharmacophore modeling, 3D-QSAR, and high-throughput virtual screening of hepatitis C virus NS5B polymerase inhibitors, J. Chem. Inf. Model. 54 (2014), pp. 539–552. doi:10.1021/ci400644r.
  • S.V. Prabhu and S.K. Singh, Energetically optimized pharmacophore modeling to identify dual negative allosteric modulators against group I mGluRs in neurodegenerative diseases, J. Biomol. Struct. Dyn. 38 (2020), pp. 2326–2337. doi:10.1080/07391102.2019.1640794.
  • Schrödinger Release 2020-1: LigPrep, Schrödinger, LLC, New York, NY, 2020.
  • I.J. Chen and N. Foloppe, Drug-like bioactive structures and conformational coverage with the ligPrep/confgen suite: Comparison to programs MOE and catalyst, J. Chem. Inf. Model 50 (2010), pp. 822–839. doi:10.1021/ci100026x.
  • P. Daisy, P. Vijayalakshmi, C. Selvaraj, S.K. Singh, and K. Saipriya, Targeting multidrug resistant Mycobacterium tuberculosis HtrA2 with identical chemical entities of fluoroquinolones, Indian J. Pharm. Sci. 74 (2012), pp. 217–222. doi:10.4103/0250-474X.106063.
  • J.F. Truchon and C.I. Bayly, Evaluating virtual screening methods: Good and bad metrics for the “early recognition” problem, J. Chem. Inf. Model. 47 (2007), pp. 488–508. doi:10.1021/ci600426e.
  • H. Patel and A. Kukol, Evaluation of a novel virtual screening strategy using receptor decoy binding sites, J. Negat. Results Biomed. 15 (2016), pp. 1–5. doi:10.1186/s12952-016-0058-8.
  • K.K. Reddy, S.K. Singh, S.K. Tripathi, and C. Selvaraj, Identification of potential HIV-1 integrase strand transfer inhibitors: In silico virtual screening and QM/MM docking studies, SAR QSAR Environ. Res. 24 (2013), pp. 581–595. doi:10.1080/1062936X.2013.772919.
  • D. Pradiba, M. Aarthy, V. Shunmugapriya, S.K. Singh, and M. Vasanthi, Structural insights into the binding mode of flavonols with the active site of matrix metalloproteinase-9 through molecular docking and molecular dynamic simulations studies, J. Biomol. Struct. Dyn. 36 (2018), pp. 3718–3739. doi:10.1080/07391102.2017.1397058.
  • V. Suryanarayanan and S.K. Singh, Assessment of dual inhibition property of newly discovered inhibitors against PCAF and GCN5 through in silico screening, molecular dynamics simulation and DFT approach, J. Recept. Signal Transduct. Res. 35 (2015), pp. 370–380. doi:10.3109/10799893.2014.956756.
  • W. Sherman, T. Day, M.P. Jacobson, R.A. Friesner, and R. Farid, Novel procedure for modeling ligand/receptor induced fit effects, J. Med. Chem. 49 (2005), pp. 534–553. doi:10.1021/jm050540c.
  • L. Delgado-Soler, J. Ariñez-Soriano, J.M. Granadino-Roldán, and J. Rubio-Martinez, Predicting binding energies of CDK6 inhibitors in the hit-to-lead process, Theor. Chem. Acc. 128 (2011), pp. 807–823. doi:10.1007/s00214-010-0857-9.
  • M. Aarthy and S.K. Singh, Discovery of potent inhibitors for the inhibition of dengue envelope protein: An in silico approach, Curr. Top. Med. Chem. 18 (2018), pp. 1585–1602. doi:10.2174/1568026618666181025100736.
  • Schrödinger Release 2020-1: Prime, Schrödinger, LLC, New York, NY, 2020.
  • R. Kumar, M. Son, R. Bavi, Y. Lee, C. Park, V. Arulalapperumal, G.P. Cao, H.H. Kim, J.K. Suh, Y.S. Kim, and Y.J. Kwon, Novel chemical scaffolds of the tumor marker AKR1B10 inhibitors discovered by 3D QSAR pharmacophore modeling, Acta Pharmacol. Sin. 36 (2015), pp. 998–1012. doi:10.1038/aps.2015.17.
  • C. Selvaraj, J. Sivakamavalli, B. Vaseeharan, P. Singh, and S.K. Singh, Structural elucidation of SrtA enzyme in Enterococcus faecalis: An emphasis on screening of potential inhibitors against the biofilm formation, Mol. Biosyst. 10 (2014), pp. 1775–1789. doi:10.1039/C3MB70613C.
  • Schrödinger Release 2020-1: QikProp, Schrödinger, LLC, New York, NY, 2020.
  • S. Sharda, P. Sarmandal, S. Cherukommu, K. Dindhoria, M. Yadav, S. Bandaru, A. Sharma, A. Sakhi, T. Vyas, T. Hussain, A. Nayarisseri, and S.K. Singh, A virtual screening approach for the identification of high affinity small molecules targeting BCR-ABL1 inhibitors for the treatment of chronic myeloid leukemia, Curr. Top Med. Chem. 17 (2017), pp. 2989–2996. doi:10.2174/1568026617666170821124512.
  • Schrödinger Release 2020-1: Desmond Molecular Dynamics System, D. E. Shaw Research, New York, NY, 2020. Maestro-Desmond Interoperability Tools, Schrödinger, New York, NY, 2020.
  • G.K. Veeramachaneni, K.K. Raj, L.M. Chalasani, J.S. Bondili, and V.R. Talluri, High-throughput virtual screening with e-pharmacophore and molecular simulations study in the designing of pancreatic lipase inhibitors, Drug Des. Devel. Ther. 9 (2015), pp. 4397–4412. doi:10.2147/DDDT.S84052.
  • A. Grover, S.P. Katiyar, S.K. Singh, V.K. Dubey, and D. Sundar, A leishmaniasis study: Structure-based screening and molecular dynamics mechanistic analysis for discovering potent inhibitors of spermidine synthase, BBA-Proteins Proteom 1824 (2012), pp. 1476–1483. doi:10.1016/j.bbapap.2012.05.016.
  • B. Shanmuganathan, V. Suryanarayanan, S. Sathya, M. Narenkumar, S.K. Singh, K. Ruckmani, and K.P. Devi, Anti-amyloidogenic and anti-apoptotic effect of α-bisabolol against Aβ induced neurotoxicity in PC12 cells, Eur. J. Med. Chem. 143 (2018), pp. 1196–1207. doi:10.1016/j.ejmech.2017.10.017.
  • S. Bandaru, M. Alvala, A. Nayarisseri, S. Sharda, H. Goud, H.P. Mundluru, and S.K. Singh, Molecular dynamics simulations reveal suboptimal binding of Salbutamol in T164I variant of β2 adrenergic receptor, PLoS One 12 (2017), pp. e0186666. doi:10.1371/journal.pone.0186666.
  • Schrödinger Release 2020-1: Jaguar, Schrödinger, LLC, New York, NY, 2020.
  • U. Panwar and S.K. Singh, Structure-based virtual screening toward the discovery of novel inhibitors for impeding the protein-protein interaction between HIV-1 integrase and human lens epithelium-derived growth factor (LEDGF/p75), J. Biomol. Struct. Dyn. 36 (2018), pp. 3199–3217. doi:10.1080/07391102.2017.1384400.
  • D.R. Motati, D. Uredi, and E.B. Watkins, The discovery and development of oxalamide and pyrrole small molecule inhibitors of gp120 and HIV entry - A review, Curr. Top. Med. Chem. 19 (2019), pp. 1650–1675. doi:10.2174/1568026619666190717163959.
  • A.M. Andrianov, G.I. Nikolaev, Y.V. Kornoushenko, W. Xu, S. Jiang, and A.V. Tuzikov, In silico identification of novel aromatic compounds as potential HIV-1 entry inhibitors mimicking cellular receptor CD4, Viruses 11 (2019), pp. 746. doi:10.3390/v11080746.
  • D.J. Castillo-Pazos, A. Romo-Mancillas, and J. Barroso-Flores, Piperazine-based HIV-1 entry inhibitors: Massive in silico library design and screening for gp120 attachment inhibitors, bioRxiv (2018), pp. 330142. doi:10.1101/330142.
  • R. Patil, S. Das, A. Stanley, L. Yadav, A. Sudhakar, and A.K. Varma, Optimized hydrophobic interactions and hydrogen bonding at the target-ligand interface leads the pathways of drug-designing, PloS One 5 (2010), pp. e12029. doi:10.1371/journal.pone.0012029.
  • H. Sun, L. Duan, F. Chen, H. Liu, Z. Wang, P. Pan, F. Zhu, J.Z.H. Zhang, and T. Hou, Assessing the performance of MM/PBSA and MM/GBSA methods. 7. entropy effects on the performance of end-point binding free energy calculation approaches, Phys. Chem. Chem. Phys. 20 (2018), pp. 14450–14460. doi:10.1039/C7CP07623A.
  • X. Du, Y. Li, Y.L. Xia, S.M. Ai, J. Liang, P. Sang, X.L. Ji, and S.Q. Liu, Insights into protein–ligand interactions: Mechanisms, models, and methods, Int. J. Mol. Sci. 17 (2016), pp. 144. doi:10.3390/ijms17020144.
  • K. Ogata, M. Hatakeyama, and S. Nakamura, Effect of atomic charges on octanol–water partition coefficient using alchemical free energy calculation, Molecules 23 (2018), pp. 425. doi:10.3390/molecules23020425.
  • R.H. Henchman, K. Tai, T. Shen, and J.A. McCammon, Properties of water molecules in the active site gorge of acetylcholinesterase from computer simulation, Biophys. J. 82 (2002), pp. 2671–2682. doi:10.1016/S0006-3495(02)75609-9.
  • B. Mathew, S. Dev, M. Joy, G.E. Mathew, A. Marathakam, and G.K. Krishnan, Refining the structural features of chromones as selective MAO‐B inhibitors: Exploration of combined pharmacophore‐based 3D‐QSAR and quantum chemical studies, ChemistrySelect 2 (2017), pp. 11645–11652. doi:10.1002/slct.201701213.
  • S.K. Singh, N. Dessalew, and P.V. Bharatam, 3D-QSAR CoMFA study on oxindole derivatives as cyclin dependent kinase 1 (CDK1) and cyclin dependent kinase 2 (CDK2) inhibitors, Med. Chem. 3 (2007), pp. 75–84. doi:10.2174/157340607779317517.
  • B. Mathew, A.A. Adeniyi, S. Dev, M. Joy, G. Ucar, G.E. Mathew, A. Singh-Pillay, and M.E.S. Soliman, Pharmacophore-based 3D-QSAR analysis of thienyl chalcones as a new class of human MAO-B inhibitors: Investigation of combined quantum chemical and molecular dynamics approach, J. Phys. Chem. B 121 (2017), pp. 1186–1203. doi:10.1021/acs.jpcb.6b09451.
  • P.K. Weiner, R. Langridge, J.M. Blaney, R. Schaefer, and P.A. Kollman, Electrostatic potential molecular surfaces, Proc Natl. Acad. Sci. USA 79 (1982), pp. 3754–3758. doi:10.1073/pnas.79.12.3754.
  • S.K. Tripathi and S.K. Singh, Insights into the structural basis of 3, 5-diaminoindazoles as CDK2 inhibitors: Prediction of binding modes and potency by QM–MM interaction, MESP and MD simulation, Mol. Biosyst. 10 (2014), pp. 2189–2201. doi:10.1039/C4MB00077C.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.