Achenbach H, Waibel R, Nkunya MH, Weenen H (1992) Antimalarial compounds from Hoslundia opposita. Phytochemistry 31:3781–3784
Article
Google Scholar
Adedeji A, Severson W, Jonsson C, Singh K, Weiss S, Sarafianos S (2013) Novel inhibitors of SARS-CoV entry acting by three distinct mechanisms. J Virol 87(14):87–8028. https://doi.org/10.1128/JVI.00998-13
Article
Google Scholar
Bagla V, McGaw L, Eloff J (2012) The antiviral activity of six South African plants traditionally used against infections in ethnoveterinary medicine. Vet Microbiol 155:198–206. https://doi.org/10.1016/j.vetmic.2011.09.015
Article
Google Scholar
Basu A, Sarkar A, Maulik U (2020) Molecular docking study of potential phytochemicals and their effects on the complex of SARS-CoV2 spike protein and human ACE2. Sci Rep 10:1–15
Article
Google Scholar
Beuscher N, Bodinet C, Neumann-Haefelin D, Marston A, Hostettmann K (1994) Antiviral activity of African medicinal plants. J Ethnopharmacol 42(2):101–109. https://doi.org/10.1016/0378-8741(94)90103-1
Article
Google Scholar
Brooks BR, Brooks CL III, Mackerell AD Jr, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor RW, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York DM, Karplus M (2009) CHARMM: the biomolecular simulation program. J Comput Chem 30(10):1545–1614. https://doi.org/10.1002/jcc.21287
Article
Google Scholar
Chen H, Du Q (2020) Potential natural compounds for preventing SARS-CoV-2 (2019-nCoV) infection
Book
Google Scholar
Chen N, Zhou M, Dong X, Qu J, Gong F, Han Y, Qiu Y, Wang J, Liu Y, Wei Y, Xia J’, Yu T, Zhang X, Zhang L (2020a) Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study. Lancet (London, England) 395:507–513. https://doi.org/10.1016/s0140-6736(20)30211-7
Article
Google Scholar
Chen YW, Yiu C-P, Wong K-Y (2020b) Prediction of the SARS-CoV-2 (2019-nCoV) 3C-like protease (3CLpro) structure: virtual screening reveals velpatasvir, ledipasvir, and other drug repurposing candidates. F1000Research 9:129. https://doi.org/10.12688/f1000research.22457.1
Article
Google Scholar
Cheng F, Li W, Zhou Y, Shen J, Wu Z, Liu G, Lee PW, Tang Y (2012) admetSAR: a comprehensive source and free tool for assessment of chemical ADMET properties. J Chem Inf Model 52:3099–3105. https://doi.org/10.1021/ci300367a
Article
Google Scholar
Cheng X, Ivanov I (2012) Molecular dynamics. Comput Toxicol 929:243–285
Coutard B, Valle C, de Lamballerie X, Canard B, Seidah NG, Decroly E (2020) The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade. Antiviral Res 176:104742. https://doi.org/10.1016/j.antiviral.2020.104742
Article
Google Scholar
Derdeyn CA, Decker JM, Sfakianos JN, Wu X, O'Brien WA, Ratner L, Kappes JC, Shaw GM, Hunter E (2000) Sensitivity of human immunodeficiency virus type 1 to the fusion inhibitor T-20 is modulated by coreceptor specificity defined by the V3 loop of gp120. J Virol 74:8358–8367. https://doi.org/10.1128/jvi.74.18.8358-8367.2000
Article
Google Scholar
Dong Y-w, Liao M-l, X-l M, Somero GN (2018) Structural flexibility and protein adaptation to temperature: Molecular dynamics analysis of malate dehydrogenases of marine molluscs. Proc Natl Acad Sci 115:1274–1279
Article
Google Scholar
Garg S, Kaul SC, Wadhwa R (2018) Cucurbitacin B and cancer intervention: chemistry, biology and mechanisms. Int J Oncol 52:19–37
Google Scholar
Gyebi GA, Adegunloye AP, Ibrahim IM, Ogunyemi OM, Afolabi SO, Ogunro OB (2020a) Prevention of SARS-CoV-2 cell entry: insight from in silico interaction of drug-like alkaloids with spike glycoprotein, human ACE2, and TMPRSS2. J Biomol Struct Dyn p 1–25. https://doi.org/10.1080/07391102.2020.1835726
Gyebi GA, Ogunro OB, Adegunloye AP, Ogunyemi OM, Afolabi SO (2020b) Potential inhibitors of coronavirus 3-chymotrypsin-like protease (3CLpro): an in silico screening of alkaloids and terpenoids from African medicinal plants. J Biomol Struct Dyn 39:3396-3408. https://doi.org/10.1080/07391102.2020.1764868
Gyebi GA, Ogunyemi OM, Ibrahim IM, Afolabi SO, Adebayo JO (2021) Dual targeting of cytokine storm and viral replication in COVID-19 by plant-derived steroidal pregnanes: an in silico perspective. Comput Biol Med 134:104406
Article
Google Scholar
Hartt JK, Liang T, Sahagun-Ruiz A, Wang JM, Gao JL, Murphy PM (2000) The HIV-1 cell entry inhibitor T-20 potently chemoattracts neutrophils by specifically activating the N-formylpeptide receptor. Biochem Biophys Res Commun 272:699–704. https://doi.org/10.1006/bbrc.2000.2846
Article
Google Scholar
Hoffmann M, Kleine-Weber H, Schroeder S, Krüger N, Herrler T, Erichsen S, Schiergens TS, Herrler G, Wu NH, Nitsche A, Müller MA, Drosten C, Pöhlmann S (2020) SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor cell. https://doi.org/10.1016/j.cell.2020.02.052
Book
Google Scholar
Hui DS, I Azhar E, Madani TA, Ntoumi F, Kock R, Dar O, Ippolito G, Mchugh TD, Memish ZA, Drosten C, Zumla A, Petersen E (2020) The continuing 2019-nCoV epidemic threat of novel coronaviruses to global health - The latest 2019 novel coronavirus outbreak in Wuhan, China. Int J Infect Dis 91:264–266. https://doi.org/10.1016/j.ijid.2020.01.009
Article
Google Scholar
Humphrey W, Dalke A, Schulten K (1996a) VMD: visual molecular dynamics. J Mol Graph 14:33–38
Article
Google Scholar
Jaeger R, Cuny E (2016) Terpenoids with special pharmacological significance: a review. Nat Prod Commun 11:1934578X1601100946. https://doi.org/10.1177/1934578X1601100946
Article
Google Scholar
Khelfaoui H, Harkati D, Saleh BA (2020) Molecular docking, molecular dynamics simulations and reactivity, studies on approved drugs library targeting ACE2 and SARS-CoV-2 binding with ACE2. J Biomol Struct Dyn p 1–17. https://doi.org/10.1080/07391102.2020.1803967
Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y, Wang W, Donini O, Cieplak P, Srinivasan J, Case DA, Cheatham TE (2000) Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res 33(12):889–897. https://doi.org/10.1021/ar000033j
Article
Google Scholar
Kyrieleis OJ, Huber R, Ong E, Oehler R, Hunter M, Madison EL, Jacob U (2007) Crystal structure of the catalytic domain of DESC1, a new member of the type II transmembrane serine proteinase family. FEBS J 274(8):2148–2160. https://doi.org/10.1111/j.1742-4658.2007.05756.x
Article
Google Scholar
Lee J, Cheng X, Swails JM, Yeom MS, Eastman PK, Lemkul JA, Wei S, Buckner J, Jeong JC, Qi Y, Jo S, Pande VS, Case DA, Brooks CL III, MacKerell AD Jr, Klauda JB, Im W (2016) CHARMM-GUI input generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM simulations using the CHARMM36 additive force field. J Chemical Theory Comput 12(1):405–413. https://doi.org/10.1021/acs.jctc.5b00935
Article
Google Scholar
Li W et al (2005) Receptor and viral determinants of SARS-coronavirus adaptation to human ACE2. EMBO J 24:1634–1643
Article
Google Scholar
Lin JH, Yamazaki M (2003) Role of P-glycoprotein in pharmacokinetics. Clin Pharmacokinet 42(1):59–98. https://doi.org/10.2165/00003088-200342010-00003
Article
Google Scholar
Lipinski CA (2000) Drug-like properties and the causes of poor solubility and poor permeability. J Pharmacol Toxicol Methods 44:235–249. https://doi.org/10.1016/s1056-8719(00)00107-6
Article
Google Scholar
Liu C, Zhou Q, Li Y, Garner LV, Watkins SP, Carter LJ, Smoot J, Gregg AC, Daniels AD, Jervey S, Albaiu D (2020) Research and development on therapeutic agents and vaccines for COVID-19 and related human coronavirus diseases. ACS Central Sci 6(3):315–331. https://doi.org/10.1021/acscentsci.0c00272
Article
Google Scholar
Mahmud SH et al (2021a) Bioinformatics and system biology approach to identify the influences of SARS-CoV-2 infections to idiopathic pulmonary fibrosis and chronic obstructive pulmonary disease patients. Brief Bioinform. bbab115, https://doi.org/10.1093/bib/bbab115
Mahmud SH, Chen W, Liu Y, Awal MA, Ahmed K, Rahman MH, Moni MA (2021b) PreDTIs: prediction of drug–target interactions based on multiple feature information using gradient boosting framework with data balancing and feature selection techniques. Brief Bioinform. bbab046, https://doi.org/10.1093/bib/bbab046
Mark P, Nilsson L (2001) Structure and dynamics of the TIP3P, SPC, and SPC/E water models at 298 K. Chem A Eur J 105(43):9954–9960. https://doi.org/10.1021/jp003020w
Article
Google Scholar
Miller BR III, McGee TD Jr, Swails JM, Homeyer N, Gohlke H, Roitberg AE (2012) MMPBSA. py: an efficient program for end-state free energy calculations. J Chemical Theory Comput 8(9):3314–3321. https://doi.org/10.1021/ct300418h
Article
Google Scholar
Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ (2009) AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem 30:2785–2791
Article
Google Scholar
Ndhlala A, Amoo S, Ncube B, Moyo M, Nair J, van Staden J (2013) Antibacterial, antifungal, and antiviral activities of African Medicinal Plants, pp 621–651. https://doi.org/10.1016/B978-0-12-405927-6.00016-3
Book
Google Scholar
Nickel J, Gohlke BO, Erehman J, Banerjee P, Rong WW, Goede A, Dunkel M, Preissner R (2014) SuperPred: update on drug classification and target prediction. Nucleic Acids Res 42:W26–W31. https://doi.org/10.1093/nar/gku477
Article
Google Scholar
O'Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR (2011) Open Babel: An open chemical toolbox. J Chem 3:33. https://doi.org/10.1186/1758-2946-3-33
Article
Google Scholar
Ogunyemi OM, Gyebi GA, Elfiky AA, Afolabi SO, Ogunro OB, Adegunloye AP, Ibrahim IM (2020) Alkaloids and flavonoids from African phytochemicals as potential inhibitors of SARS-Cov-2 RNA-dependent RNA polymerase: an in silico perspective. Antiviral Chem Chemother 28:2040206620984076
Article
Google Scholar
Ojo O, Oluyege J, Famurewa O (2009) Antiviral properties of two Nigerian plants. Afr J Plant Sci 3:157–159
Google Scholar
Park JY, Kim JH, Kim YM, Jeong HJ, Kim DW, Park KH, Kwon HJ, Park SJ, Lee WS, Ryu YB (2012) Tanshinones as selective and slow-binding inhibitors for SARS-CoV cysteine proteases. Bioorg Med Chem 20:5928–5935. https://doi.org/10.1016/j.bmc.2012.07.038
Article
Google Scholar
Perez A, Morrone JA, Simmerling C, Dill KA (2016) Advances in free-energy-based simulations of protein folding and ligand binding. Curr Opin Struct Biol 36:25–31. https://doi.org/10.1016/j.sbi.2015.12.002
Article
Google Scholar
Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kalé L, Schulten K (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26(16):1781–1802. https://doi.org/10.1002/jcc.20289
Article
Google Scholar
Pushkaran AC, Melge AR, Puthiyedath R, Mohan CG (2021) A phytochemical-based medication search for the SARS-CoV-2 infection by molecular docking models towards spike glycoproteins and main proteases. RSC Adv 11:12003–12014
Article
Google Scholar
Ryu YB, Park SJ, Kim YM, Lee JY, Seo WD, Chang JS, Park KH, Rho MC, Lee WS (2010) SARS-CoV 3CLpro inhibitory effects of quinone-methide triterpenes from Tripterygium regelii. Bioorg Med Chem Lett 20:1873–1876. https://doi.org/10.1016/j.bmcl.2010.01.152
Article
Google Scholar
Salentin S, Schreiber S, Haupt VJ, Adasme MF, Schroeder M (2015) PLIP: fully automated protein–ligand interaction profiler. Nucleic Acids Res 43(W1):W443–W447. https://doi.org/10.1093/nar/gkv315
Article
Google Scholar
Sanchez-Linares I, Perez-Sanchez H, Cecilia JM, Garcia JM (2012) High-throughput parallel blind virtual screening using BINDSURF. BMC Bioinform 13(Suppl 14):S13. https://doi.org/10.1186/1471-2105-13-s14-s13
Article
Google Scholar
Shang J et al. (2020) Structural basis for receptor recognition by the novel coronavirus from Wuhan
Book
Google Scholar
Shen L, Niu J, Wang C, Huang B, Wang W, Zhu N, Deng Y, Wang H, Ye F, Cen S, Tan W (2019) High-throughput screening and identification of potent broad-spectrum inhibitors of coronaviruses. J Virol 93:e00023-19. https://doi.org/10.1128/jvi.00023-19
Sinha S, Wang SM (2020) Classification of VUS and unclassified variants in BRCA1 BRCT repeats by molecular dynamics simulation. Comput Struct Biotechnol J 18:723–736
Article
Google Scholar
Sonawane K et al. (2020) Homology modeling and docking studies of TMPRSS2 with experimentally known inhibitors camostat mesylate, nafamostat and bromhexine hydrochloride to control SARS-Coronavirus-2
Google Scholar
Srinivasan S, Cui H, Gao Z, Liu M, Lu S, Mkandawire W, Narykov O, Sun M, Korkin D (2020) Structural genomics of SARS-CoV-2 indicates evolutionary conserved functional regions of viral proteins. Viruses 12:360. https://doi.org/10.3390/v12040360
Suomivuori C-M et al (2020) Molecular mechanism of biased signaling in a prototypical G protein–coupled receptor. Science (New York, NY) 367:881–887
Article
Google Scholar
Taniguchi Y, Nishikawa H, Maeda N, Terada Y (2020) Breathlessness, pleural effusions, fibromas, and Meigs syndrome: look beyond the chest and don't delay! Lancet 395:e32. https://doi.org/10.1016/S0140-6736(20)30111-2
Article
Google Scholar
Taz TA, Ahmed K, Paul BK, Al-Zahrani FA, Mahmud SH, Moni MA (2021a) Identification of biomarkers and pathways for the SARS-CoV-2 infections that make complexities in pulmonary arterial hypertension patients. Brief Bioinform 22:1451–1465
Article
Google Scholar
Taz TA, Ahmed K, Paul BK, Kawsar M, Aktar N, Mahmud SH, Moni MA (2021b) Network-based identification genetic effect of SARS-CoV-2 infections to Idiopathic pulmonary fibrosis (IPF) patients. Brief Bioinform 22:1254–1266
Article
Google Scholar
Towler P, Staker B, Prasad SG, Menon S, Tang J, Parsons T, Ryan D, Fisher M, Williams D, Dales NA, Patane MA, Pantoliano MW (2004) ACE2 X-ray structures reveal a large hinge-bending motion important for inhibitor binding and catalysis. J Biol Chem 279:17996–18007. https://doi.org/10.1074/jbc.M311191200
Article
Google Scholar
Trott O, Olson AJ (2010) AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 31:455–461. https://doi.org/10.1002/jcc.21334
Article
Google Scholar
Tubiana T, Carvaillo J-C, Boulard Y, Bressanelli S (2018) TTClust: a versatile molecular simulation trajectory clustering program with graphical summaries. J Chem Inf Model 58(11):2178–2182. https://doi.org/10.1021/acs.jcim.8b00512
Article
Google Scholar
Tung N, Kwon H-J, Kim J-H, Ra J, Ding Y, Kim J, Kim YH (2010) Antiinfluenza diarylheptanoids from the bark of Alnus japonica. Bioorg Med Chem Lett 20(3):1000–1003. https://doi.org/10.1016/j.bmcl.2009.12.057
Article
Google Scholar
Vardhan S, Sahoo SK (2021) Virtual screening by targeting proteolytic sites of furin and TMPRSS2 to propose potential compounds obstructing the entry of SARS-CoV-2 virus into human host cells. J Tradit Complement Med. https://doi.org/10.1016/j.jtcme.2021.04.001
Wan Y, Shang J, Graham R, Baric RS, Li F (2020) Receptor recognition by the novel coronavirus from Wuhan: an analysis based on decade-long structural studies of SARS coronavirus. J Virol 94(7):e00127–e00120. https://doi.org/10.1128/JVI.00127-20
Article
Google Scholar
Wang Q et al (2020) Structural and functional basis of SARS-CoV-2 entry by using human ACE2. Cell 181:894–904. e899
Article
Google Scholar
Wen CC, Kuo YH, Jan JT, Liang PH, Wang SY, Liu HG, Lee CK, Chang ST, Kuo CJ, Lee SS, Hou CC, Hsiao PW, Chien SC, Shyur LF, Yang NS (2007) Specific plant terpenoids and lignoids possess potent antiviral activities against severe acute respiratory syndrome coronavirus. J Med Chem 50:4087–4095. https://doi.org/10.1021/jm070295s
Article
Google Scholar
WHO (2020) Report of the WHO-China joint mission on coronavirus disease 2019 (COVID-19) Geneva
Google Scholar
Wrapp D, Wang N, Corbett KS, Goldsmith JA, Hsieh CL, Abiona O, Graham BS, McLellan JS (2020) Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science (New York, NY) 367:eabb2507. https://doi.org/10.1126/science.abb2507
Article
Google Scholar
Wu C, Liu Y, Yang Y, Zhang P, Zhong W, Wang Y, Wang Q, Xu Y, Li M, Li X, Zheng M, Chen L, Li H (2020) Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods. Acta Pharmaceut Sinica B 10(5):766–788. https://doi.org/10.1016/j.apsb.2020.02.008
Article
Google Scholar
Wu K, Li W, Peng G, Li F (2009) Crystal structure of NL63 respiratory coronavirus receptor-binding domain complexed with its human receptor. Proc Natl Acad Sci 106:19970–19974
Article
Google Scholar
Xiao S, Tian Z, Wang Y, Si L, Zhang L, Zhou D (2018) Recent progress in the antiviral activity and mechanism study of pentacyclic triterpenoids and their derivatives. Med Res Rev 38(3):951–976. https://doi.org/10.1002/med.21484
Article
Google Scholar
Yamamoto M, Matsuyama S, Li X, Takeda M, Kawaguchi Y, Inoue J-i, Matsuda Z (2016) Identification of nafamostat as a potent inhibitor of Middle East respiratory syndrome coronavirus S protein-mediated membrane fusion using the split-protein-based cell-cell fusion assay. Antimicrob Agents Chemother 60(11):6532–6539. https://doi.org/10.1128/AAC.01043-16
Article
Google Scholar
Yuan Y, Cao D, Zhang Y, Ma J, Qi J, Wang Q, Lu G, Wu Y, Yan J, Shi Y, Zhang X, Gao GF (2017) Cryo-EM structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains. Nat Commun 8:15092. https://doi.org/10.1038/ncomms15092
Article
Google Scholar
Zanin L, Saraceno G, Panciani PP, Renisi G, Signorini L, Migliorati K, Fontanella MM (2020) SARS-CoV-2 can induce brain and spine demyelinating lesions. Acta Neurochir 162(7):1491–1494. https://doi.org/10.1007/s00701-020-04374-x
Article
Google Scholar
Zhang H, Penninger JM, Li Y, Zhong N, Slutsky AS (2020) Angiotensin-converting enzyme 2 (ACE2) as a SARS-CoV-2 receptor: molecular mechanisms and potential therapeutic target. Intensive Care Med 46(4):586–590. https://doi.org/10.1007/s00134-020-05985-9
Article
Google Scholar
Zhao H, Caflisch A (2015) Molecular dynamics in drug design. Eur J Med Chem 91:4–14. https://doi.org/10.1016/j.ejmech.2014.08.004
Article
Google Scholar
Zhou P et al (2020) A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 579:270–273
Article
Google Scholar
Zhou Y, Vedantham P, Lu K, Agudelo J, Carrion R Jr, Nunneley JW, Barnard D, Pöhlmann S, McKerrow JH, Renslo AR, Simmons G (2015) Protease inhibitors targeting coronavirus and filovirus entry. Antiviral Res 116:76–84. https://doi.org/10.1016/j.antiviral.2015.01.011
Article
Google Scholar