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Validating ADME QSAR Models Using Marketed Drugs.

SLAS discovery : advancing life sciences R & D

Siramshetty V, Williams J, Nguyễn ÐT, Neyra J, Southall N, Mathé E, Xu X, Shah P.
PMID: 34176369
SLAS Discov. 2021 Dec;26(10):1326-1336. doi: 10.1177/24725552211017520. Epub 2021 Jun 26.

Problems with drug ADME are responsible for many clinical failures. By understanding the ADME properties of marketed drugs and modeling how chemical structure contributes to these inherent properties, we can help new projects reduce their risk profiles. Kinetic aqueous...

Cite
Siramshetty V, Williams J, Nguyễn ÐT, et al. Validating ADME QSAR Models Using Marketed Drugs. SLAS Discov. 2021;26(10):1326-1336doi: 10.1177/24725552211017520.
Siramshetty, V., Williams, J., Nguyễn, �. �. T., Neyra, J., Southall, N., Mathé, E., Xu, X., & Shah, P. (2021). Validating ADME QSAR Models Using Marketed Drugs. SLAS discovery : advancing life sciences R & D, 26(10), 1326-1336. https://doi.org/10.1177/24725552211017520
Siramshetty, Vishal, et al. "Validating ADME QSAR Models Using Marketed Drugs." SLAS discovery : advancing life sciences R & D vol. 26,10 (2021): 1326-1336. doi: https://doi.org/10.1177/24725552211017520
Siramshetty V, Williams J, Nguyễn ÐT, Neyra J, Southall N, Mathé E, Xu X, Shah P. Validating ADME QSAR Models Using Marketed Drugs. SLAS Discov. 2021 Dec;26(10):1326-1336. doi: 10.1177/24725552211017520. Epub 2021 Jun 26. PMID: 34176369.
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A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research.

bioRxiv : the preprint server for biology

Zahoránszky-Kőhalmi G, Siramshetty VB, Kumar P, Gurumurthy M, Grillo B, Mathew B, Metaxatos D, Backus M, Mierzwa T, Simon R, Grishagin I, Brovold L, Mathé EA, Hall MD, Michael SG, Godfrey AG, Mestres J, Jensen LJ, Oprea TI.
PMID: 33173863
bioRxiv. 2020 Nov 05; doi: 10.1101/2020.11.04.369041.

MOTIVATION: In the event of an outbreak due to an emerging pathogen, time is of the essence to contain or to mitigate the spread of the disease. Drug repositioning is one of the strategies that has the potential to...

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Zahoránszky-Kőhalmi G, Siramshetty VB, Kumar P, et al. A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research. bioRxiv. 2020;doi: 10.1101/2020.11.04.369041.
Zahoránszky-Kőhalmi, G., Siramshetty, V. B., Kumar, P., Gurumurthy, M., Grillo, B., Mathew, B., Metaxatos, D., Backus, M., Mierzwa, T., Simon, R., Grishagin, I., Brovold, L., Mathé, E. A., Hall, M. D., Michael, S. G., Godfrey, A. G., Mestres, J., Jensen, L. J., & Oprea, T. I. (2020). A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research. bioRxiv : the preprint server for biology, . https://doi.org/10.1101/2020.11.04.369041
Zahoránszky-Kőhalmi, Gergely, et al. "A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research." bioRxiv : the preprint server for biology vol. (2020). doi: https://doi.org/10.1101/2020.11.04.369041
Zahoránszky-Kőhalmi G, Siramshetty VB, Kumar P, Gurumurthy M, Grillo B, Mathew B, Metaxatos D, Backus M, Mierzwa T, Simon R, Grishagin I, Brovold L, Mathé EA, Hall MD, Michael SG, Godfrey AG, Mestres J, Jensen LJ, Oprea TI. A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research. bioRxiv. 2020 Nov 05; doi: 10.1101/2020.11.04.369041. PMID: 33173863; PMCID: PMC7654851.
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NCATS Inxight Drugs: a comprehensive and curated portal for translational research.

Nucleic acids research

Siramshetty VB, Grishagin I, Nguyễn ÐT, Peryea T, Skovpen Y, Stroganov O, Katzel D, Sheils T, Jadhav A, Mathé EA, Southall NT.
PMID: 34648031
Nucleic Acids Res. 2022 Jan 07;50:D1307-D1316. doi: 10.1093/nar/gkab918.

The United States has a complex regulatory scheme for marketing drugs. Understanding drug regulatory status is a daunting task that requires integrating data from many sources from the United States Food and Drug Administration (FDA), US government publications, and...

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Siramshetty VB, Grishagin I, Nguyễn ÐT, et al. NCATS Inxight Drugs: a comprehensive and curated portal for translational research. Nucleic Acids Res. 2022;50:D1307-D1316doi: 10.1093/nar/gkab918.
Siramshetty, V. B., Grishagin, I., Nguyễn, �. �. T., Peryea, T., Skovpen, Y., Stroganov, O., Katzel, D., Sheils, T., Jadhav, A., Mathé, E. A., & Southall, N. T. (2022). NCATS Inxight Drugs: a comprehensive and curated portal for translational research. Nucleic acids research, 50D1307-D1316. https://doi.org/10.1093/nar/gkab918
Siramshetty, Vishal B, et al. "NCATS Inxight Drugs: a comprehensive and curated portal for translational research." Nucleic acids research vol. 50 (2022): D1307-D1316. doi: https://doi.org/10.1093/nar/gkab918
Siramshetty VB, Grishagin I, Nguyễn ÐT, Peryea T, Skovpen Y, Stroganov O, Katzel D, Sheils T, Jadhav A, Mathé EA, Southall NT. NCATS Inxight Drugs: a comprehensive and curated portal for translational research. Nucleic Acids Res. 2022 Jan 07;50:D1307-D1316. doi: 10.1093/nar/gkab918. PMID: 34648031; PMCID: PMC8728186.
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NCATS Inxight Drugs: a comprehensive and curated portal for translational research.

Nucleic acids research

Siramshetty VB, Grishagin I, Nguyễn ÐT, Peryea T, Skovpen Y, Stroganov O, Katzel D, Sheils T, Jadhav A, Mathé EA, Southall NT.
PMID: 34648031
Nucleic Acids Res. 2022 Jan 07;50:D1307-D1316. doi: 10.1093/nar/gkab918.

The United States has a complex regulatory scheme for marketing drugs. Understanding drug regulatory status is a daunting task that requires integrating data from many sources from the United States Food and Drug Administration (FDA), US government publications, and...

Cite
Siramshetty VB, Grishagin I, Nguyễn ÐT, et al. NCATS Inxight Drugs: a comprehensive and curated portal for translational research. Nucleic Acids Res. 2022;50:D1307-D1316doi: 10.1093/nar/gkab918.
Siramshetty, V. B., Grishagin, I., Nguyễn, �. �. T., Peryea, T., Skovpen, Y., Stroganov, O., Katzel, D., Sheils, T., Jadhav, A., Mathé, E. A., & Southall, N. T. (2022). NCATS Inxight Drugs: a comprehensive and curated portal for translational research. Nucleic acids research, 50D1307-D1316. https://doi.org/10.1093/nar/gkab918
Siramshetty, Vishal B, et al. "NCATS Inxight Drugs: a comprehensive and curated portal for translational research." Nucleic acids research vol. 50 (2022): D1307-D1316. doi: https://doi.org/10.1093/nar/gkab918
Siramshetty VB, Grishagin I, Nguyễn ÐT, Peryea T, Skovpen Y, Stroganov O, Katzel D, Sheils T, Jadhav A, Mathé EA, Southall NT. NCATS Inxight Drugs: a comprehensive and curated portal for translational research. Nucleic Acids Res. 2022 Jan 07;50:D1307-D1316. doi: 10.1093/nar/gkab918. PMID: 34648031.
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Validating ADME QSAR Models Using Marketed Drugs.

SLAS discovery : advancing life sciences R & D

Siramshetty V, Williams J, Nguyễn ÐT, Neyra J, Southall N, Mathé E, Xu X, Shah P.
PMID: 34176369
SLAS Discov. 2021 Dec;26(10):1326-1336. doi: 10.1177/24725552211017520. Epub 2021 Jun 26.

Problems with drug ADME are responsible for many clinical failures. By understanding the ADME properties of marketed drugs and modeling how chemical structure contributes to these inherent properties, we can help new projects reduce their risk profiles. Kinetic aqueous...

Cite
Siramshetty V, Williams J, Nguyễn ÐT, et al. Validating ADME QSAR Models Using Marketed Drugs. SLAS Discov. 2021;26(10):1326-1336doi: 10.1177/24725552211017520.
Siramshetty, V., Williams, J., Nguyễn, �. �. T., Neyra, J., Southall, N., Mathé, E., Xu, X., & Shah, P. (2021). Validating ADME QSAR Models Using Marketed Drugs. SLAS discovery : advancing life sciences R & D, 26(10), 1326-1336. https://doi.org/10.1177/24725552211017520
Siramshetty, Vishal, et al. "Validating ADME QSAR Models Using Marketed Drugs." SLAS discovery : advancing life sciences R & D vol. 26,10 (2021): 1326-1336. doi: https://doi.org/10.1177/24725552211017520
Siramshetty V, Williams J, Nguyễn ÐT, Neyra J, Southall N, Mathé E, Xu X, Shah P. Validating ADME QSAR Models Using Marketed Drugs. SLAS Discov. 2021 Dec;26(10):1326-1336. doi: 10.1177/24725552211017520. Epub 2021 Jun 26. PMID: 34176369.
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Computational methods for prediction of in vitro effects of new chemical structures.

Journal of cheminformatics

Banerjee P, Siramshetty VB, Drwal MN, Preissner R.
PMID: 28316649
J Cheminform. 2016 Sep 29;8:51. doi: 10.1186/s13321-016-0162-2. eCollection 2016.

BACKGROUND: With a constant increase in the number of new chemicals synthesized every year, it becomes important to employ the most reliable and fast in silico screening methods to predict their safety and activity profiles. In recent years, in...

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Banerjee P, Siramshetty VB, Drwal MN, et al. Computational methods for prediction of in vitro effects of new chemical structures. J Cheminform. 2016;8:51doi: 10.1186/s13321-016-0162-2.
Banerjee, P., Siramshetty, V. B., Drwal, M. N., & Preissner, R. (2016). Computational methods for prediction of in vitro effects of new chemical structures. Journal of cheminformatics, 851. https://doi.org/10.1186/s13321-016-0162-2
Banerjee, Priyanka, et al. "Computational methods for prediction of in vitro effects of new chemical structures." Journal of cheminformatics vol. 8 (2016): 51. doi: https://doi.org/10.1186/s13321-016-0162-2
Banerjee P, Siramshetty VB, Drwal MN, Preissner R. Computational methods for prediction of in vitro effects of new chemical structures. J Cheminform. 2016 Sep 29;8:51. doi: 10.1186/s13321-016-0162-2. eCollection 2016. PMID: 28316649; PMCID: PMC5043617.
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NCATS Inxight Drugs: a comprehensive and curated portal for translational research.

Nucleic acids research

Siramshetty VB, Grishagin I, Nguyễn ÐT, Peryea T, Skovpen Y, Stroganov O, Katzel D, Sheils T, Jadhav A, Mathé EA, Southall NT.
PMID: 34648031
Nucleic Acids Res. 2021 Oct 14; doi: 10.1093/nar/gkab918. Epub 2021 Oct 14.

The United States has a complex regulatory scheme for marketing drugs. Understanding drug regulatory status is a daunting task that requires integrating data from many sources from the United States Food and Drug Administration (FDA), US government publications, and...

Cite
Siramshetty VB, Grishagin I, Nguyễn ÐT, et al. NCATS Inxight Drugs: a comprehensive and curated portal for translational research. Nucleic Acids Res. 2021;doi: 10.1093/nar/gkab918.
Siramshetty, V. B., Grishagin, I., Nguyễn, �. �. T., Peryea, T., Skovpen, Y., Stroganov, O., Katzel, D., Sheils, T., Jadhav, A., Mathé, E. A., & Southall, N. T. (2021). NCATS Inxight Drugs: a comprehensive and curated portal for translational research. Nucleic acids research, . https://doi.org/10.1093/nar/gkab918
Siramshetty, Vishal B, et al. "NCATS Inxight Drugs: a comprehensive and curated portal for translational research." Nucleic acids research vol. (2021). doi: https://doi.org/10.1093/nar/gkab918
Siramshetty VB, Grishagin I, Nguyễn ÐT, Peryea T, Skovpen Y, Stroganov O, Katzel D, Sheils T, Jadhav A, Mathé EA, Southall NT. NCATS Inxight Drugs: a comprehensive and curated portal for translational research. Nucleic Acids Res. 2021 Oct 14; doi: 10.1093/nar/gkab918. Epub 2021 Oct 14. PMID: 34648031.
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Using in vitro ADME data for lead compound selection: An emphasis on PAMPA pH 5 permeability and oral bioavailability.

Bioorganic & medicinal chemistry

Williams J, Siramshetty V, Nguyễn ÐT, Padilha EC, Kabir M, Yu KR, Wang AQ, Zhao T, Itkin M, Shinn P, Mathé EA, Xu X, Shah P.
PMID: 35030421
Bioorg Med Chem. 2022 Jan 05;56:116588. doi: 10.1016/j.bmc.2021.116588. Epub 2022 Jan 05.

Membrane permeability plays an important role in oral drug absorption. Caco-2 and Madin-Darby Canine Kidney (MDCK) cell culture systems have been widely used for assessing intestinal permeability. Since most drugs are absorbed passively, Parallel Artificial Membrane Permeability Assay (PAMPA)...

Cite
Williams J, Siramshetty V, Nguyễn ÐT, et al. Using in vitro ADME data for lead compound selection: An emphasis on PAMPA pH 5 permeability and oral bioavailability. Bioorg Med Chem. 2022;56:116588doi: 10.1016/j.bmc.2021.116588.
Williams, J., Siramshetty, V., Nguyễn, �. �. T., Padilha, E. C., Kabir, M., Yu, K. R., Wang, A. Q., Zhao, T., Itkin, M., Shinn, P., Mathé, E. A., Xu, X., & Shah, P. (2022). Using in vitro ADME data for lead compound selection: An emphasis on PAMPA pH 5 permeability and oral bioavailability. Bioorganic & medicinal chemistry, 56116588. https://doi.org/10.1016/j.bmc.2021.116588
Williams, Jordan, et al. "Using in vitro ADME data for lead compound selection: An emphasis on PAMPA pH 5 permeability and oral bioavailability." Bioorganic & medicinal chemistry vol. 56 (2022): 116588. doi: https://doi.org/10.1016/j.bmc.2021.116588
Williams J, Siramshetty V, Nguyễn ÐT, Padilha EC, Kabir M, Yu KR, Wang AQ, Zhao T, Itkin M, Shinn P, Mathé EA, Xu X, Shah P. Using in vitro ADME data for lead compound selection: An emphasis on PAMPA pH 5 permeability and oral bioavailability. Bioorg Med Chem. 2022 Jan 05;56:116588. doi: 10.1016/j.bmc.2021.116588. Epub 2022 Jan 05. PMID: 35030421.
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Using in vitro ADME data for lead compound selection: An emphasis on PAMPA pH 5 permeability and oral bioavailability.

Bioorganic & medicinal chemistry

Williams J, Siramshetty V, Nguyễn ÐT, Padilha EC, Kabir M, Yu KR, Wang AQ, Zhao T, Itkin M, Shinn P, Mathé EA, Xu X, Shah P.
PMID: 35030421
Bioorg Med Chem. 2022 Jan 05;56:116588. doi: 10.1016/j.bmc.2021.116588. Epub 2022 Jan 05.

Membrane permeability plays an important role in oral drug absorption. Caco-2 and Madin-Darby Canine Kidney (MDCK) cell culture systems have been widely used for assessing intestinal permeability. Since most drugs are absorbed passively, Parallel Artificial Membrane Permeability Assay (PAMPA)...

Cite
Williams J, Siramshetty V, Nguyễn ÐT, et al. Using in vitro ADME data for lead compound selection: An emphasis on PAMPA pH 5 permeability and oral bioavailability. Bioorg Med Chem. 2022;56:116588doi: 10.1016/j.bmc.2021.116588.
Williams, J., Siramshetty, V., Nguyễn, �. �. T., Padilha, E. C., Kabir, M., Yu, K. R., Wang, A. Q., Zhao, T., Itkin, M., Shinn, P., Mathé, E. A., Xu, X., & Shah, P. (2022). Using in vitro ADME data for lead compound selection: An emphasis on PAMPA pH 5 permeability and oral bioavailability. Bioorganic & medicinal chemistry, 56116588. https://doi.org/10.1016/j.bmc.2021.116588
Williams, Jordan, et al. "Using in vitro ADME data for lead compound selection: An emphasis on PAMPA pH 5 permeability and oral bioavailability." Bioorganic & medicinal chemistry vol. 56 (2022): 116588. doi: https://doi.org/10.1016/j.bmc.2021.116588
Williams J, Siramshetty V, Nguyễn ÐT, Padilha EC, Kabir M, Yu KR, Wang AQ, Zhao T, Itkin M, Shinn P, Mathé EA, Xu X, Shah P. Using in vitro ADME data for lead compound selection: An emphasis on PAMPA pH 5 permeability and oral bioavailability. Bioorg Med Chem. 2022 Jan 05;56:116588. doi: 10.1016/j.bmc.2021.116588. Epub 2022 Jan 05. PMID: 35030421.
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Predicting liver cytosol stability of small molecules.

Journal of cheminformatics

Shah P, Siramshetty VB, Zakharov AV, Southall NT, Xu X, Nguyen DT.
PMID: 33431020
J Cheminform. 2020 Apr 07;12(1):21. doi: 10.1186/s13321-020-00426-7.

Over the last few decades, chemists have become skilled at designing compounds that avoid cytochrome P (CYP) 450 mediated metabolism. Typical screening assays are performed in liver microsomal fractions and it is possible to overlook the contribution of cytosolic...

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Shah P, Siramshetty VB, Zakharov AV, et al. Predicting liver cytosol stability of small molecules. J Cheminform. 2020;12(1):21doi: 10.1186/s13321-020-00426-7.
Shah, P., Siramshetty, V. B., Zakharov, A. V., Southall, N. T., Xu, X., & Nguyen, D. T. (2020). Predicting liver cytosol stability of small molecules. Journal of cheminformatics, 12(1), 21. https://doi.org/10.1186/s13321-020-00426-7
Shah, Pranav, et al. "Predicting liver cytosol stability of small molecules." Journal of cheminformatics vol. 12,1 (2020): 21. doi: https://doi.org/10.1186/s13321-020-00426-7
Shah P, Siramshetty VB, Zakharov AV, Southall NT, Xu X, Nguyen DT. Predicting liver cytosol stability of small molecules. J Cheminform. 2020 Apr 07;12(1):21. doi: 10.1186/s13321-020-00426-7. PMID: 33431020; PMCID: PMC7140498.
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