Skip to main content
Top
Published in: Mathematics in Computer Science 4/2021

16-06-2021

Mathematical Multidimensional Modelling and Structural Artificial Intelligence Pipelines Provide Insights for the Designing of Highly Specific AntiSARS-CoV2 Agents

Authors: Dimitrios Vlachakis, Panayiotis Vlamos

Published in: Mathematics in Computer Science | Issue 4/2021

Log in

Activate our intelligent search to find suitable subject content or patents.

search-config
loading …

Abstract

COVID19 is the most impactful pandemic of recent times worldwide. It is a highly infectious disease that is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 virus), To date there is specific drug nor vaccination against COVID19. Therefor the need for novel and pioneering anti-COVID19 is of paramount importance. In this direction, computer-aided drug design constitutes a very promising antiviral approach for the discovery and analysis of drugs and molecules with biological activity against SARS-CoV2. In silico modelling takes advantage of the massive amounts of biological and chemical data available on the nature of the interactions between the targeted systems and molecules, as well as the rapid progress of computational tools and software. Herein, we describe the potential of the merging of mathematical modelling, artificial intelligence and learning techniques into seamless computational pipelines for the rapid and efficient discovery and design of potent anti- SARS-CoV-2 modulators.

Dont have a licence yet? Then find out more about our products and how to get one now:

Springer Professional "Wirtschaft+Technik"

Online-Abonnement

Mit Springer Professional "Wirtschaft+Technik" erhalten Sie Zugriff auf:

  • über 102.000 Bücher
  • über 537 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Finance + Banking
  • Management + Führung
  • Marketing + Vertrieb
  • Maschinenbau + Werkstoffe
  • Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

Springer Professional "Wirtschaft"

Online-Abonnement

Mit Springer Professional "Wirtschaft" erhalten Sie Zugriff auf:

  • über 67.000 Bücher
  • über 340 Zeitschriften

aus folgenden Fachgebieten:

  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Finance + Banking
  • Management + Führung
  • Marketing + Vertrieb
  • Versicherung + Risiko




Jetzt Wissensvorsprung sichern!

Springer Professional "Technik"

Online-Abonnement

Mit Springer Professional "Technik" erhalten Sie Zugriff auf:

  • über 67.000 Bücher
  • über 390 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Maschinenbau + Werkstoffe




 

Jetzt Wissensvorsprung sichern!

Literature
1.
go back to reference Acharya, C., Coop, A., Polli, J.E., Mackerell Jr., A.D.: Recent advances in ligand-based drug design: relevance and utility of the conformationally sampled pharmacophore approach. Curr. Comput. Aided Drug Des. 7(1), 10–22 (2011) Acharya, C., Coop, A., Polli, J.E., Mackerell Jr., A.D.: Recent advances in ligand-based drug design: relevance and utility of the conformationally sampled pharmacophore approach. Curr. Comput. Aided Drug Des. 7(1), 10–22 (2011)
2.
go back to reference Adhikari, S.P., Meng, S., Wu, Y.J., Mao, Y.P., Ye, R.X., Wang, Q.Z., Sun, C., Sylvia, S., Rozelle, S., Raat, H., Zhou, H.: Epidemiology, causes, clinical manifestation and diagnosis, prevention and control of coronavirus disease (COVID-19) during the early outbreak period: a scoping review. Infect Dis. Poverty 9(1), 29 (2020) Adhikari, S.P., Meng, S., Wu, Y.J., Mao, Y.P., Ye, R.X., Wang, Q.Z., Sun, C., Sylvia, S., Rozelle, S., Raat, H., Zhou, H.: Epidemiology, causes, clinical manifestation and diagnosis, prevention and control of coronavirus disease (COVID-19) during the early outbreak period: a scoping review. Infect Dis. Poverty 9(1), 29 (2020)
3.
go back to reference Akamatsu, M.: Current state and perspectives of 3D-QSAR. Curr. Top. Med. Chem. 2(12), 1381–1394 (2002) Akamatsu, M.: Current state and perspectives of 3D-QSAR. Curr. Top. Med. Chem. 2(12), 1381–1394 (2002)
4.
go back to reference Allen, R., Moore, H.: Perspectives on the role of mathematics in drug discovery and development. Bull. Math. Biol. 81(9), 3425–3435 (2019) Allen, R., Moore, H.: Perspectives on the role of mathematics in drug discovery and development. Bull. Math. Biol. 81(9), 3425–3435 (2019)
5.
go back to reference Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J.: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25(17), 3389–3402 (1997) Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J.: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25(17), 3389–3402 (1997)
6.
go back to reference Belouzard, S., Chu, V.C., Whittaker, G.R.: Activation of the SARS coronavirus spike protein via sequential proteolytic cleavage at two distinct sites. Proc. Natl. Acad. Sci. U S A 106(14), 5871–5876 (2009) Belouzard, S., Chu, V.C., Whittaker, G.R.: Activation of the SARS coronavirus spike protein via sequential proteolytic cleavage at two distinct sites. Proc. Natl. Acad. Sci. U S A 106(14), 5871–5876 (2009)
7.
go back to reference Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E.: The protein data bank. Nucleic Acids Res. 28(1), 235–242 (2000) Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E.: The protein data bank. Nucleic Acids Res. 28(1), 235–242 (2000)
8.
go back to reference Bosch, B.J., van der Zee, R., de Haan, C.A., Rottier, P.J.: The coronavirus spike protein is a class I virus fusion protein: structural and functional characterization of the fusion core complex. J. Virol. 77(16), 8801–8811 (2003) Bosch, B.J., van der Zee, R., de Haan, C.A., Rottier, P.J.: The coronavirus spike protein is a class I virus fusion protein: structural and functional characterization of the fusion core complex. J. Virol. 77(16), 8801–8811 (2003)
9.
go back to reference Burbidge, R., Trotter, M., Buxton, B., Holden, S.: Drug design by machine learning: support vector machines for pharmaceutical data analysis. Comput. Chem. 26(1), 5–14 (2001) Burbidge, R., Trotter, M., Buxton, B., Holden, S.: Drug design by machine learning: support vector machines for pharmaceutical data analysis. Comput. Chem. 26(1), 5–14 (2001)
10.
go back to reference Cao, C., Liu, F., Tan, H., Song, D., Shu, W., Li, W., Zhou, Y., Bo, X., Xie, Z.: Deep learning and its applications in biomedicine. Genomics Proteomics Bioinf. 16(1), 17–32 (2018) Cao, C., Liu, F., Tan, H., Song, D., Shu, W., Li, W., Zhou, Y., Bo, X., Xie, Z.: Deep learning and its applications in biomedicine. Genomics Proteomics Bioinf. 16(1), 17–32 (2018)
11.
go back to reference Chan-Yeung, M., Xu, R.H.: SARS: epidemiology. Respirology 8(Suppl), S9–14 (2003) Chan-Yeung, M., Xu, R.H.: SARS: epidemiology. Respirology 8(Suppl), S9–14 (2003)
12.
go back to reference Chan, H.C.S., Shan, H., Dahoun, T., Vogel, H., Yuan, S.: Advancing drug discovery via artificial intelligence. Trends Pharmacol. Sci. 40(8), 592–604 (2019) Chan, H.C.S., Shan, H., Dahoun, T., Vogel, H., Yuan, S.: Advancing drug discovery via artificial intelligence. Trends Pharmacol. Sci. 40(8), 592–604 (2019)
13.
go back to reference Chen, H., Engkvist, O., Wang, Y., Olivecrona, M., Blaschke, T.: The rise of deep learning in drug discovery. Drug Discov. Today 23(6), 1241–1250 (2018) Chen, H., Engkvist, O., Wang, Y., Olivecrona, M., Blaschke, T.: The rise of deep learning in drug discovery. Drug Discov. Today 23(6), 1241–1250 (2018)
14.
go back to reference Chen, L., Morrow, J.K., Tran, H.T., Phatak, S.S., Du-Cuny, L., Zhang, S.: From laptop to benchtop to bedside: structure-based drug design on protein targets. Curr. Pharm. Des. 18(9), 1217–1239 (2012) Chen, L., Morrow, J.K., Tran, H.T., Phatak, S.S., Du-Cuny, L., Zhang, S.: From laptop to benchtop to bedside: structure-based drug design on protein targets. Curr. Pharm. Des. 18(9), 1217–1239 (2012)
15.
go back to reference Chen, N., Zhou, M., Dong, X., Qu, J., Gong, F., Han, Y., Qiu, Y., Wang, J., Liu, Y., Wei, Y., Xia, J.a, Yu, T., Zhang, X., Zhang, L.: Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study. Lancet 395(10223), 507–513 (2020) Chen, N., Zhou, M., Dong, X., Qu, J., Gong, F., Han, Y., Qiu, Y., Wang, J., Liu, Y., Wei, Y., Xia, J.a, Yu, T., Zhang, X., Zhang, L.: Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study. Lancet 395(10223), 507–513 (2020)
16.
go back to reference Cheng, F., Kovács, I.A., Barabási, A.-L.: Network-based prediction of drug combinations. Nat. Commun. 10(1), 1197 (2019) Cheng, F., Kovács, I.A., Barabási, A.-L.: Network-based prediction of drug combinations. Nat. Commun. 10(1), 1197 (2019)
17.
go back to reference Cheng, Z.J., Shan, J.: 2019 Novel coronavirus: where we are and what we know. Infection 48(2), 155–163 (2020)MathSciNet Cheng, Z.J., Shan, J.: 2019 Novel coronavirus: where we are and what we know. Infection 48(2), 155–163 (2020)MathSciNet
18.
go back to reference Colijn, C., Jones, N., Johnston, I.G., Yaliraki, S., Barahona, M.: Toward precision healthcare: context and mathematical challenges. Front. Physiol. 8, 136 (2017) Colijn, C., Jones, N., Johnston, I.G., Yaliraki, S., Barahona, M.: Toward precision healthcare: context and mathematical challenges. Front. Physiol. 8, 136 (2017)
19.
go back to reference Davenport, T., Kalakota, R.: The potential for artificial intelligence in healthcare. Future Healthc. J. 6(2), 94–98 (2019) Davenport, T., Kalakota, R.: The potential for artificial intelligence in healthcare. Future Healthc. J. 6(2), 94–98 (2019)
20.
go back to reference Dias, R., Torkamani, A.: Artificial intelligence in clinical and genomic diagnostics. Genome Med. 11(1), 70 (2019) Dias, R., Torkamani, A.: Artificial intelligence in clinical and genomic diagnostics. Genome Med. 11(1), 70 (2019)
21.
go back to reference Friesner, R.A., Murphy, R.B., Repasky, M.P., Frye, L.L., Greenwood, J.R., Halgren, T.A., Sanschagrin, P.C., Mainz, D.T.: Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. J. Med. Chem. 49(21), 6177–6196 (2006) Friesner, R.A., Murphy, R.B., Repasky, M.P., Frye, L.L., Greenwood, J.R., Halgren, T.A., Sanschagrin, P.C., Mainz, D.T.: Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. J. Med. Chem. 49(21), 6177–6196 (2006)
22.
go back to reference Fischer, H.P.: Mathematical modeling of complex biological systems: from parts lists to understanding systems behavior. Alcohol Res. Health : J. Natl. Inst. Alcohol Abuse Alcohol. 31(1), 49–59 (2008) Fischer, H.P.: Mathematical modeling of complex biological systems: from parts lists to understanding systems behavior. Alcohol Res. Health : J. Natl. Inst. Alcohol Abuse Alcohol. 31(1), 49–59 (2008)
23.
go back to reference Ginsburg, G.S., Phillips, K.A.: Precision medicine: from science to value. Health Aff. (Project Hope) 37(5), 694–701 (2018) Ginsburg, G.S., Phillips, K.A.: Precision medicine: from science to value. Health Aff. (Project Hope) 37(5), 694–701 (2018)
24.
go back to reference Gobburu, J.V.S., Lesko, L.J.: Quantitative disease, drug, and trial models. Annu. Rev. Pharmacol. Toxicol. 49(1), 291–301 (2009) Gobburu, J.V.S., Lesko, L.J.: Quantitative disease, drug, and trial models. Annu. Rev. Pharmacol. Toxicol. 49(1), 291–301 (2009)
25.
go back to reference Holford, N.: Pharmacodynamic principles and the time course of immediate drug effects. Transl. Clin. Pharmacol. 25(4), 157–61 (2017) Holford, N.: Pharmacodynamic principles and the time course of immediate drug effects. Transl. Clin. Pharmacol. 25(4), 157–61 (2017)
26.
go back to reference Huang, P., Liu, T., Huang, L., Liu, H., Lei, M., Xu, W., Hu, X., Chen, J., Liu, B.: Use of chest CT in combination with negative RT-PCR assay for the 2019 novel coronavirus but high clinical suspicion. Radiology 295(1), 22–23 (2020) Huang, P., Liu, T., Huang, L., Liu, H., Lei, M., Xu, W., Hu, X., Chen, J., Liu, B.: Use of chest CT in combination with negative RT-PCR assay for the 2019 novel coronavirus but high clinical suspicion. Radiology 295(1), 22–23 (2020)
27.
go back to reference Illergard, K., Ardell, D.H., Elofsson, A.: Structure is three to ten times more conserved than sequence-a study of structural response in protein cores. Proteins 77(3), 499–508 (2009) Illergard, K., Ardell, D.H., Elofsson, A.: Structure is three to ten times more conserved than sequence-a study of structural response in protein cores. Proteins 77(3), 499–508 (2009)
28.
go back to reference Jin, Y.H., Cai, L., Cheng, Z.S., Cheng, H., Deng, T., Fan, Y.P., Fang, C., Huang, D., Huang, L.Q., Huang, Q., Han, Y., Hu, B., Hu, F., Li, B.H., Li, Y.R., Liang, K., Lin, L.K., Luo, L.S., Ma, J., Ma, L.L., Peng, Z.Y., Pan, Y.B., Pan, Z.Y., Ren, X.Q., Sun, H.M., Wang, Y., Wang, Y.Y., Weng, H., Wei, C.J., Wu, D.F., Xia, J., Xiong, Y., Xu, H.B., Yao, X.M., Yuan, Y.F., Ye, T.S., Zhang, X.C., Zhang, Y.W., Zhang, Y.G., Zhang, H.M., Zhao, Y., Zhao, M.J., Zi, H., Zeng, X.T., Wang, Y.Y., Wang, X.H., FTZHOWUNC Management, E-BMCOCIE Research Team: M. Promotive association for and C. health: a rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version). Mil. Med. Res. 7(1), 4 (2020) Jin, Y.H., Cai, L., Cheng, Z.S., Cheng, H., Deng, T., Fan, Y.P., Fang, C., Huang, D., Huang, L.Q., Huang, Q., Han, Y., Hu, B., Hu, F., Li, B.H., Li, Y.R., Liang, K., Lin, L.K., Luo, L.S., Ma, J., Ma, L.L., Peng, Z.Y., Pan, Y.B., Pan, Z.Y., Ren, X.Q., Sun, H.M., Wang, Y., Wang, Y.Y., Weng, H., Wei, C.J., Wu, D.F., Xia, J., Xiong, Y., Xu, H.B., Yao, X.M., Yuan, Y.F., Ye, T.S., Zhang, X.C., Zhang, Y.W., Zhang, Y.G., Zhang, H.M., Zhao, Y., Zhao, M.J., Zi, H., Zeng, X.T., Wang, Y.Y., Wang, X.H., FTZHOWUNC Management, E-BMCOCIE Research Team: M. Promotive association for and C. health: a rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version). Mil. Med. Res. 7(1), 4 (2020)
29.
go back to reference Kuntz, I.D., Blaney, J.M., Oatley, S.J., Langridge, R., Ferrin, T.E.: A geometric approach to macromolecule-ligand interactions. J. Mol. Biol. 161(2), 269–288 (1982) Kuntz, I.D., Blaney, J.M., Oatley, S.J., Langridge, R., Ferrin, T.E.: A geometric approach to macromolecule-ligand interactions. J. Mol. Biol. 161(2), 269–288 (1982)
30.
go back to reference Kurogi, Y., Guner, O.F.: Pharmacophore modeling and three-dimensional database searching for drug design using catalyst. Curr. Med. Chem. 8(9), 1035–1055 (2001) Kurogi, Y., Guner, O.F.: Pharmacophore modeling and three-dimensional database searching for drug design using catalyst. Curr. Med. Chem. 8(9), 1035–1055 (2001)
31.
go back to reference Lalonde, R.L., Kowalski, K.G., Hutmacher, M.M., Ewy, W., Nichols, D.J., Milligan, P.A., et al.: Model-based drug development. Clin. Pharmaco. Ther. 82(1), 21–32 (2007) Lalonde, R.L., Kowalski, K.G., Hutmacher, M.M., Ewy, W., Nichols, D.J., Milligan, P.A., et al.: Model-based drug development. Clin. Pharmaco. Ther. 82(1), 21–32 (2007)
32.
go back to reference Lavezzi, S.M., Borella, E., Carrara, L., De Nicolao, G., Magni, P., Poggesi, I.: Mathematical modeling of efficacy and safety for anticancer drugs clinical development. Expert Opin. Drug Discov. 13(1), 5–21 (2018) Lavezzi, S.M., Borella, E., Carrara, L., De Nicolao, G., Magni, P., Poggesi, I.: Mathematical modeling of efficacy and safety for anticancer drugs clinical development. Expert Opin. Drug Discov. 13(1), 5–21 (2018)
33.
go back to reference Leelananda, S.P., Lindert, S.: Computational methods in drug discovery. Beilstein J. Org. Chem. 12, 2694–2718 (2016) Leelananda, S.P., Lindert, S.: Computational methods in drug discovery. Beilstein J. Org. Chem. 12, 2694–2718 (2016)
34.
go back to reference Li, W., Tang, Y., Liu, H., Cheng, J., Zhu, W., Jiang, H.: Probing ligand binding modes of human cytochrome P450 2J2 by homology modeling, molecular dynamics simulation, and flexible molecular docking. Proteins 71(2), 938–949 (2008) Li, W., Tang, Y., Liu, H., Cheng, J., Zhu, W., Jiang, H.: Probing ligand binding modes of human cytochrome P450 2J2 by homology modeling, molecular dynamics simulation, and flexible molecular docking. Proteins 71(2), 938–949 (2008)
35.
go back to reference Li, Y., Kong, Y., Zhang, M., Yan, A., Liu, Z.: Using support vector machine (SVM) for classification of selectivity of H1N1 neuraminidase inhibitors. Mol. Inform. 35(3–4), 116–124 (2016) Li, Y., Kong, Y., Zhang, M., Yan, A., Liu, Z.: Using support vector machine (SVM) for classification of selectivity of H1N1 neuraminidase inhibitors. Mol. Inform. 35(3–4), 116–124 (2016)
36.
go back to reference Lu, H.: Drug treatment options for the 2019-new coronavirus (2019-nCoV). Biosci. Trends 14(1), 69–71 (2020) Lu, H.: Drug treatment options for the 2019-new coronavirus (2019-nCoV). Biosci. Trends 14(1), 69–71 (2020)
37.
go back to reference Malathi, K., Ramaiah, S.: Bioinformatics approaches for new drug discovery: a review. Biotechnol. Genet. Eng. Rev. 34(2), 243–260 (2018) Malathi, K., Ramaiah, S.: Bioinformatics approaches for new drug discovery: a review. Biotechnol. Genet. Eng. Rev. 34(2), 243–260 (2018)
38.
go back to reference Maltarollo, V.G., Kronenberger, T., Espinoza, G.Z., Oliveira, P.R., Honorio, K.M.: Advances with support vector machines for novel drug discovery. Expert Opin. Drug Discov. 14(1), 23–33 (2019) Maltarollo, V.G., Kronenberger, T., Espinoza, G.Z., Oliveira, P.R., Honorio, K.M.: Advances with support vector machines for novel drug discovery. Expert Opin. Drug Discov. 14(1), 23–33 (2019)
40.
go back to reference Marti-Renom, M.A., Stuart, A.C., Fiser, A., Sanchez, R., Melo, F., Sali, A.: Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 29, 291–325 (2000) Marti-Renom, M.A., Stuart, A.C., Fiser, A., Sanchez, R., Melo, F., Sali, A.: Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 29, 291–325 (2000)
41.
go back to reference Moore, H., Allen, R.: What can mathematics do for drug development? Bull. Math. Biol. 81(9), 3421–3424 (2019)MATH Moore, H., Allen, R.: What can mathematics do for drug development? Bull. Math. Biol. 81(9), 3421–3424 (2019)MATH
42.
go back to reference Nichols, J.A., Herbert Chan, H.W., Baker, M.A.B.: Machine learning: applications of artificial intelligence to imaging and diagnosis. Biophys. Rev. 11(1), 111–118 (2019) Nichols, J.A., Herbert Chan, H.W., Baker, M.A.B.: Machine learning: applications of artificial intelligence to imaging and diagnosis. Biophys. Rev. 11(1), 111–118 (2019)
44.
go back to reference Ou-Yang, S.S., Lu, J.Y., Kong, X.Q., Liang, Z.J., Luo, C., Jiang, H.: Computational drug discovery. Acta Pharmacol. Sin 33(9), 1131–1140 (2012) Ou-Yang, S.S., Lu, J.Y., Kong, X.Q., Liang, Z.J., Luo, C., Jiang, H.: Computational drug discovery. Acta Pharmacol. Sin 33(9), 1131–1140 (2012)
45.
go back to reference Ou, X., Liu, Y., Lei, X., Li, P., Mi, D., Ren, L., Guo, L., Guo, R., Chen, T., Hu, J., Xiang, Z., Mu, Z., Chen, X., Chen, J., Hu, K., Jin, Q., Wang, J., Qian, Z.: Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with SARS-CoV. Nat. Commun. 11(1), 1620 (2020) Ou, X., Liu, Y., Lei, X., Li, P., Mi, D., Ren, L., Guo, L., Guo, R., Chen, T., Hu, J., Xiang, Z., Mu, Z., Chen, X., Chen, J., Hu, K., Jin, Q., Wang, J., Qian, Z.: Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with SARS-CoV. Nat. Commun. 11(1), 1620 (2020)
46.
go back to reference Pagadala, N.S., Syed, K., Tuszynski, J.: Software for molecular docking: a review. Biophys. Rev. 9(2), 91–102 (2017) Pagadala, N.S., Syed, K., Tuszynski, J.: Software for molecular docking: a review. Biophys. Rev. 9(2), 91–102 (2017)
47.
go back to reference Patel, K., Simpson, J.A., Batty, K.T., Zaloumis, S., Kirkpatrick, C.M.: Modelling the time course of antimalarial parasite killing: a tour of animal and human models, translation and challenges. Br. J. Clin. Pharmacol. 79(1), 97–107 (2015) Patel, K., Simpson, J.A., Batty, K.T., Zaloumis, S., Kirkpatrick, C.M.: Modelling the time course of antimalarial parasite killing: a tour of animal and human models, translation and challenges. Br. J. Clin. Pharmacol. 79(1), 97–107 (2015)
48.
go back to reference Paul, S.M., Mytelka, D.S., Dunwiddie, C.T., Persinger, C.C., Munos, B.H., Lindborg, S.R., Schacht, A.L.: How to improve R&D productivity: the pharmaceutical industry’s grand challenge. Nat. Rev. Drug Discov. 9(3), 203–214 (2010) Paul, S.M., Mytelka, D.S., Dunwiddie, C.T., Persinger, C.C., Munos, B.H., Lindborg, S.R., Schacht, A.L.: How to improve R&D productivity: the pharmaceutical industry’s grand challenge. Nat. Rev. Drug Discov. 9(3), 203–214 (2010)
49.
go back to reference Pickett, B.E., Sadat, E.L., Zhang, Y., Noronha, J.M., Squires, R.B., Hunt, V., Liu, M., Kumar, S., Zaremba, S., Gu, Z., Zhou, L., Larson, C.N., Dietrich, J., Klem, E.B., Scheuermann, R.H.: ViPR: an open bioinformatics database and analysis resource for virology research. Nucleic Acids Res. 40, D593–598 (2012) Pickett, B.E., Sadat, E.L., Zhang, Y., Noronha, J.M., Squires, R.B., Hunt, V., Liu, M., Kumar, S., Zaremba, S., Gu, Z., Zhou, L., Larson, C.N., Dietrich, J., Klem, E.B., Scheuermann, R.H.: ViPR: an open bioinformatics database and analysis resource for virology research. Nucleic Acids Res. 40, D593–598 (2012)
50.
go back to reference Popova, M., Isayev, O., Tropsha, A.: Deep reinforcement learning for de novo drug design. Sci. Adv. 4(7), eaap7885 (2018) Popova, M., Isayev, O., Tropsha, A.: Deep reinforcement learning for de novo drug design. Sci. Adv. 4(7), eaap7885 (2018)
51.
go back to reference Pushpakom, S., Iorio, F., Eyers, P.A., Escott, K.J., Hopper, S., Wells, A., Doig, A., Guilliams, T., Latimer, J., McNamee, C., Norris, A., Sanseau, P., Cavalla, D., Pirmohamed, M.: Drug repurposing: progress, challenges and recommendations. Nat. Rev. Drug Discov. 18(1), 41–58 (2019) Pushpakom, S., Iorio, F., Eyers, P.A., Escott, K.J., Hopper, S., Wells, A., Doig, A., Guilliams, T., Latimer, J., McNamee, C., Norris, A., Sanseau, P., Cavalla, D., Pirmohamed, M.: Drug repurposing: progress, challenges and recommendations. Nat. Rev. Drug Discov. 18(1), 41–58 (2019)
52.
go back to reference Raval, A., Piana, S., Eastwood, M.P., Dror, R.O., Shaw, D.E.: Refinement of protein structure homology models via long, all-atom molecular dynamics simulations. Proteins 80(8), 2071–2079 (2012) Raval, A., Piana, S., Eastwood, M.P., Dror, R.O., Shaw, D.E.: Refinement of protein structure homology models via long, all-atom molecular dynamics simulations. Proteins 80(8), 2071–2079 (2012)
53.
go back to reference Réda, C., Kaufmann, E., Delahaye-Duriez, A.: Machine learning applications in drug development. Comput. Struct. Biotechnol. J. 18, 241–252 (2020) Réda, C., Kaufmann, E., Delahaye-Duriez, A.: Machine learning applications in drug development. Comput. Struct. Biotechnol. J. 18, 241–252 (2020)
54.
go back to reference Ristevski, B., Chen, M.: Big data analytics in medicine and healthcare. J. Integr. Bioinform. 15(3), 20170030 (2018) Ristevski, B., Chen, M.: Big data analytics in medicine and healthcare. J. Integr. Bioinform. 15(3), 20170030 (2018)
55.
go back to reference Rothan, H.A., Byrareddy, S.N.: The epidemiology and pathogenesis of coronavirus disease (COVID-19) outbreak. J. Autoimmun. 109, 102433 (2020) Rothan, H.A., Byrareddy, S.N.: The epidemiology and pathogenesis of coronavirus disease (COVID-19) outbreak. J. Autoimmun. 109, 102433 (2020)
56.
go back to reference Rothe, C., Schunk, M., Sothmann, P., Bretzel, G., Froeschl, G., Wallrauch, C., Zimmer, T., Thiel, V., Janke, C., Guggemos, W., Seilmaier, M., Drosten, C., Vollmar, P., Zwirglmaier, K., Zange, S., Wolfel, R., Hoelscher, M.: Transmission of 2019-nCoV infection from an asymptomatic contact in Germany. N. Engl. J. Med. 382(10), 970–971 (2020) Rothe, C., Schunk, M., Sothmann, P., Bretzel, G., Froeschl, G., Wallrauch, C., Zimmer, T., Thiel, V., Janke, C., Guggemos, W., Seilmaier, M., Drosten, C., Vollmar, P., Zwirglmaier, K., Zange, S., Wolfel, R., Hoelscher, M.: Transmission of 2019-nCoV infection from an asymptomatic contact in Germany. N. Engl. J. Med. 382(10), 970–971 (2020)
57.
go back to reference Salahudeen, M.S., Nishtala, P.S.: An overview of pharmacodynamic modelling, ligand-binding approach and its application in clinical practice. Saudi Pharm. J. 25(2), 165–75 (2017) Salahudeen, M.S., Nishtala, P.S.: An overview of pharmacodynamic modelling, ligand-binding approach and its application in clinical practice. Saudi Pharm. J. 25(2), 165–75 (2017)
58.
go back to reference Schames, J.R., Henchman, R.H., Siegel, J.S., Sotriffer, C.A., Ni, H., McCammon, J.A.: Discovery of a novel binding trench in HIV integrase. J. Med. Chem. 47(8), 1879–1881 (2004) Schames, J.R., Henchman, R.H., Siegel, J.S., Sotriffer, C.A., Ni, H., McCammon, J.A.: Discovery of a novel binding trench in HIV integrase. J. Med. Chem. 47(8), 1879–1881 (2004)
59.
go back to reference Schneider, G.: Automating drug discovery. Nat. Rev. Drug Discov. 17(2), 97–113 (2018) Schneider, G.: Automating drug discovery. Nat. Rev. Drug Discov. 17(2), 97–113 (2018)
60.
go back to reference Schneider, P., Walters, W.P., Plowright, A.T., Sieroka, N., Listgarten, J., Goodnow, R.A., Fisher, J., Jansen, J.M., Duca, J.S., Rush, T.S., Zentgraf, M., Hill, J.E., Krutoholow, E., Kohler, M., Blaney, J., Funatsu, K., Luebkemann, C., Schneider, G.: Rethinking drug design in the artificial intelligence era. Nat. Rev. Drug Discov. 19(5), 353–364 (2020) Schneider, P., Walters, W.P., Plowright, A.T., Sieroka, N., Listgarten, J., Goodnow, R.A., Fisher, J., Jansen, J.M., Duca, J.S., Rush, T.S., Zentgraf, M., Hill, J.E., Krutoholow, E., Kohler, M., Blaney, J., Funatsu, K., Luebkemann, C., Schneider, G.: Rethinking drug design in the artificial intelligence era. Nat. Rev. Drug Discov. 19(5), 353–364 (2020)
61.
go back to reference Sethi, A., Joshi, K., Sasikala, K., Alvala, M.: Molecular docking in modern drug discovery: principles and recent applications. In: Gaitonde, V., Karmakar, P., Trivedi, A. (eds.) Drug Discovery and Development - New Advances. IntechOpen, London (2020) Sethi, A., Joshi, K., Sasikala, K., Alvala, M.: Molecular docking in modern drug discovery: principles and recent applications. In: Gaitonde, V., Karmakar, P., Trivedi, A. (eds.) Drug Discovery and Development - New Advances. IntechOpen, London (2020)
62.
go back to reference Shang, J., Ye, G., Shi, K., Wan, Y., Luo, C., Aihara, H., Geng, Q., Auerbach, A., Li, F.: Structural basis of receptor recognition by SARS-CoV-2. Nature 581(7807), 221–224 (2020) Shang, J., Ye, G., Shi, K., Wan, Y., Luo, C., Aihara, H., Geng, Q., Auerbach, A., Li, F.: Structural basis of receptor recognition by SARS-CoV-2. Nature 581(7807), 221–224 (2020)
63.
go back to reference Singh, B., Mal, G., Gautam, S.K., Mukesh M.: Computer-aided drug discovery. Advances in Animal Biotechnology (2019) Singh, B., Mal, G., Gautam, S.K., Mukesh M.: Computer-aided drug discovery. Advances in Animal Biotechnology (2019)
64.
go back to reference Singhal, T.: A review of coronavirus disease-2019 (COVID-19). Indian J. Pediatr. 87(4), 281–286 (2020) Singhal, T.: A review of coronavirus disease-2019 (COVID-19). Indian J. Pediatr. 87(4), 281–286 (2020)
65.
go back to reference Slater, H.C., Okell, L.C., Ghani, A.C.: Mathematical modelling to guide drug development for malaria elimination. Trends Parasitol. 33(3), 175–184 (2017) Slater, H.C., Okell, L.C., Ghani, A.C.: Mathematical modelling to guide drug development for malaria elimination. Trends Parasitol. 33(3), 175–184 (2017)
66.
go back to reference Sliwoski, G., Kothiwale, S., Meiler, J., Lowe Jr., E.W.: Computational methods in drug discovery. Pharmacol. Rev. 66(1), 334–395 (2013) Sliwoski, G., Kothiwale, S., Meiler, J., Lowe Jr., E.W.: Computational methods in drug discovery. Pharmacol. Rev. 66(1), 334–395 (2013)
67.
go back to reference Smellie, A., Teig, S.L., Towbin, P.: Poling: promoting conformational variation. J. Comput. Chem. 16(2), 171–187 (1995) Smellie, A., Teig, S.L., Towbin, P.: Poling: promoting conformational variation. J. Comput. Chem. 16(2), 171–187 (1995)
68.
go back to reference Sohrabi, C., Alsafi, Z., O’Neill, N., Khan, M., Kerwan, A., Al-Jabir, A., Iosifidis, C., Agha, R.: World Health Organization declares global emergency: a review of the 2019 novel coronavirus (COVID-19). Int. J. Surg. 76, 71–76 (2020) Sohrabi, C., Alsafi, Z., O’Neill, N., Khan, M., Kerwan, A., Al-Jabir, A., Iosifidis, C., Agha, R.: World Health Organization declares global emergency: a review of the 2019 novel coronavirus (COVID-19). Int. J. Surg. 76, 71–76 (2020)
69.
go back to reference Sonawane, A.R., Weiss, S.T., Glass, K., Sharma, A.: Network medicine in the age of biomedical big data. Front. Genet. 10, 294 (2019) Sonawane, A.R., Weiss, S.T., Glass, K., Sharma, A.: Network medicine in the age of biomedical big data. Front. Genet. 10, 294 (2019)
70.
go back to reference Tang, Y., Zhu, W., Chen, K., Jiang, H.: New technologies in computer-aided drug design: toward target identification and new chemical entity discovery. Drug Discov. Today Technol. 3(3), 307–313 (2006) Tang, Y., Zhu, W., Chen, K., Jiang, H.: New technologies in computer-aided drug design: toward target identification and new chemical entity discovery. Drug Discov. Today Technol. 3(3), 307–313 (2006)
71.
go back to reference Toots, M., Yoon, J.J., Cox, R.M., Hart, M., Sticher, Z.M., Makhsous, N., Plesker, R., Barrena, A.H., Reddy, P.G., Mitchell, D.G., Shean, R.C., Bluemling, G.R., Kolykhalov, A.A., Greninger, A.L., Natchus, M.G., Painter, G.R., Plemper, R.K.: Characterization of orally efficacious influenza drug with high resistance barrier in ferrets and human airway epithelia. Sci. Transl. Med. 11, 515 (2019) Toots, M., Yoon, J.J., Cox, R.M., Hart, M., Sticher, Z.M., Makhsous, N., Plesker, R., Barrena, A.H., Reddy, P.G., Mitchell, D.G., Shean, R.C., Bluemling, G.R., Kolykhalov, A.A., Greninger, A.L., Natchus, M.G., Painter, G.R., Plemper, R.K.: Characterization of orally efficacious influenza drug with high resistance barrier in ferrets and human airway epithelia. Sci. Transl. Med. 11, 515 (2019)
72.
go back to reference Usha, T., Shanmugarajan, D., Goyal, A.K., Kumar, C.S., Middha, S.K.: Recent updates on computer-aided drug discovery: time for a paradigm shift. Curr. Top Med. Chem. 17(30), 3296–3307 (2017) Usha, T., Shanmugarajan, D., Goyal, A.K., Kumar, C.S., Middha, S.K.: Recent updates on computer-aided drug discovery: time for a paradigm shift. Curr. Top Med. Chem. 17(30), 3296–3307 (2017)
73.
go back to reference Vamathevan, J., Clark, D., Czodrowski, P., Dunham, I., Ferran, E., Lee, G., Li, B., Madabhushi, A., Shah, P., Spitzer, M., Zhao, S.: Applications of machine learning in drug discovery and development. Nat. Rev. Drug Discov. 18(6), 463–477 (2019) Vamathevan, J., Clark, D., Czodrowski, P., Dunham, I., Ferran, E., Lee, G., Li, B., Madabhushi, A., Shah, P., Spitzer, M., Zhao, S.: Applications of machine learning in drug discovery and development. Nat. Rev. Drug Discov. 18(6), 463–477 (2019)
74.
go back to reference Verdonk, M.L., Chessari, G., Cole, J.C., Hartshorn, M.J., Murray, C.W., Nissink, J.W., Taylor, R.D., Taylor, R.: Modeling water molecules in protein-ligand docking using GOLD. J. Med. Chem. 48(20), 6504–6515 (2005) Verdonk, M.L., Chessari, G., Cole, J.C., Hartshorn, M.J., Murray, C.W., Nissink, J.W., Taylor, R.D., Taylor, R.: Modeling water molecules in protein-ligand docking using GOLD. J. Med. Chem. 48(20), 6504–6515 (2005)
75.
go back to reference Vilar, S., Cozza, G., Moro, S.: Medicinal chemistry and the molecular operating environment (MOE): application of QSAR and molecular docking to drug discovery. Curr. Top Med. Chem. 8(18), 1555–1572 (2008) Vilar, S., Cozza, G., Moro, S.: Medicinal chemistry and the molecular operating environment (MOE): application of QSAR and molecular docking to drug discovery. Curr. Top Med. Chem. 8(18), 1555–1572 (2008)
76.
go back to reference Wang, F., Liu, D., Wang, H., Luo, C., Zheng, M., Liu, H., Zhu, W., Luo, X., Zhang, J., Jiang, H.: Computational screening for active compounds targeting protein sequences: methodology and experimental validation. J. Chem. Inf. Model 51(11), 2821–2828 (2011) Wang, F., Liu, D., Wang, H., Luo, C., Zheng, M., Liu, H., Zhu, W., Luo, X., Zhang, J., Jiang, H.: Computational screening for active compounds targeting protein sequences: methodology and experimental validation. J. Chem. Inf. Model 51(11), 2821–2828 (2011)
77.
go back to reference Wang, L., Gu, Q., Zheng, X., Ye, J., Liu, Z., Li, J., Hu, X., Hagler, A., Xu, J.: Discovery of new selective human aldose reductase inhibitors through virtual screening multiple binding pocket conformations. J. Chem. Inf. Model 53(9), 2409–2422 (2013) Wang, L., Gu, Q., Zheng, X., Ye, J., Liu, Z., Li, J., Hu, X., Hagler, A., Xu, J.: Discovery of new selective human aldose reductase inhibitors through virtual screening multiple binding pocket conformations. J. Chem. Inf. Model 53(9), 2409–2422 (2013)
78.
go back to reference Wang, M., Cao, R., Zhang, L., Yang, X., Liu, J., Xu, M., Shi, Z., Hu, Z., Zhong, W., Xiao, G.: Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro. Cell Res. 30(3), 269–271 (2020) Wang, M., Cao, R., Zhang, L., Yang, X., Liu, J., Xu, M., Shi, Z., Hu, Z., Zhong, W., Xiao, G.: Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro. Cell Res. 30(3), 269–271 (2020)
79.
go back to reference Wang, Z., Deisboeck, T.S.: Mathematical modeling in cancer drug discovery. Drug Discov. Today 19(2), 145–150 (2014) Wang, Z., Deisboeck, T.S.: Mathematical modeling in cancer drug discovery. Drug Discov. Today 19(2), 145–150 (2014)
82.
go back to reference Wolber, G., Langer, T.: LigandScout: 3-D Pharmacophores derived from protein-bound ligands and their use as virtual screening filters. J. Chem. Inf. Model. 45(1), 160–169 (2005) Wolber, G., Langer, T.: LigandScout: 3-D Pharmacophores derived from protein-bound ligands and their use as virtual screening filters. J. Chem. Inf. Model. 45(1), 160–169 (2005)
83.
go back to reference Xiang, Z.: Advances in homology protein structure modeling. Curr. Protein Pept. Sci. 7(3), 217–227 (2006) Xiang, Z.: Advances in homology protein structure modeling. Curr. Protein Pept. Sci. 7(3), 217–227 (2006)
84.
go back to reference Xu, H., Aldrich, M.C., Chen, Q., Liu, H., Peterson, N.B., Dai, Q., Levy, M., Shah, A., Han, X., Ruan, X., Jiang, M., Li, Y., Julien, J.S., Warner, J., Friedman, C., Roden, D.M., Denny, J.C.: Validating drug repurposing signals using electronic health records: a case study of metformin associated with reduced cancer mortality. J. Am. Med. Inf. Assoc. : JAMIA 22(1), 179–191 (2015) Xu, H., Aldrich, M.C., Chen, Q., Liu, H., Peterson, N.B., Dai, Q., Levy, M., Shah, A., Han, X., Ruan, X., Jiang, M., Li, Y., Julien, J.S., Warner, J., Friedman, C., Roden, D.M., Denny, J.C.: Validating drug repurposing signals using electronic health records: a case study of metformin associated with reduced cancer mortality. J. Am. Med. Inf. Assoc. : JAMIA 22(1), 179–191 (2015)
85.
go back to reference Xue, H., Li, J., Xie, H., Wang, Y.: Review of drug repositioning approaches and resources. Int. J. Biol. Sci. 14(10), 1232–1244 (2018) Xue, H., Li, J., Xie, H., Wang, Y.: Review of drug repositioning approaches and resources. Int. J. Biol. Sci. 14(10), 1232–1244 (2018)
86.
go back to reference Yu, R.H., Cao, Y.X.: A method to determine pharmacokinetic parameters based on andante constant-rate intravenous infusion. Sci. Rep. 7(1), 13279 (2017) Yu, R.H., Cao, Y.X.: A method to determine pharmacokinetic parameters based on andante constant-rate intravenous infusion. Sci. Rep. 7(1), 13279 (2017)
87.
go back to reference Yuki, K., Fujiogi, M., Koutsogiannaki, S.: COVID-19 pathophysiology: a review. Clin. Immunol. (Orlando, Fla.) 215, 108427 (2020) Yuki, K., Fujiogi, M., Koutsogiannaki, S.: COVID-19 pathophysiology: a review. Clin. Immunol. (Orlando, Fla.) 215, 108427 (2020)
88.
go back to reference Zhang, Y., Geng, X., Tan, Y., Li, Q., Xu, C., Xu, J., Hao, L., Zeng, Z., Luo, X., Liu, F., Wang, H.: New understanding of the damage of SARS-CoV-2 infection outside the respiratory system. Biomed. Pharmacother. = Biomed. Pharmacother. 127, 110195 (2020) Zhang, Y., Geng, X., Tan, Y., Li, Q., Xu, C., Xu, J., Hao, L., Zeng, Z., Luo, X., Liu, F., Wang, H.: New understanding of the damage of SARS-CoV-2 infection outside the respiratory system. Biomed. Pharmacother. = Biomed. Pharmacother. 127, 110195 (2020)
89.
go back to reference Zhao, H., Caflisch, A.: Molecular dynamics in drug design. Eur. J. Med. Chem. 91, 4–14 (2015) Zhao, H., Caflisch, A.: Molecular dynamics in drug design. Eur. J. Med. Chem. 91, 4–14 (2015)
90.
go back to reference Zhu, H.: Big data and artificial intelligence modeling for drug discovery. Annu. Rev. Pharmacol. Toxicol. 60(1), 573–589 (2020) Zhu, H.: Big data and artificial intelligence modeling for drug discovery. Annu. Rev. Pharmacol. Toxicol. 60(1), 573–589 (2020)
Metadata
Title
Mathematical Multidimensional Modelling and Structural Artificial Intelligence Pipelines Provide Insights for the Designing of Highly Specific AntiSARS-CoV2 Agents
Authors
Dimitrios Vlachakis
Panayiotis Vlamos
Publication date
16-06-2021
Publisher
Springer International Publishing
Published in
Mathematics in Computer Science / Issue 4/2021
Print ISSN: 1661-8270
Electronic ISSN: 1661-8289
DOI
https://doi.org/10.1007/s11786-021-00517-0

Other articles of this Issue 4/2021

Mathematics in Computer Science 4/2021 Go to the issue

Premium Partner