Reliable and accurate prediction of basic pK $$_a$$ values in nitrogen compounds: the pK $$_a$$ shift in supramolecular systems as a case study
Tóm tắt
This article presents a quantitative structure–activity relationship (QSAR) approach for predicting the acid dissociation constant (pK
$$_a$$
) of nitrogenous compounds, including those within supramolecular complexes based on cucurbiturils. The model combines low-cost quantum mechanical calculations with QSAR methodology and linear regressions to achieve accurate predictions for a broad range of nitrogen-containing compounds. The model was developed using a diverse dataset of 130 nitrogenous compounds and exhibits excellent predictive performance, with a high coefficient of determination (R
$$^2$$
) of 0.9905, low standard error (s) of 0.3066, and high Fisher statistic (F) of 2142. The model outperforms existing methods, such as Chemaxon software and previous studies, in terms of accuracy and its ability to handle heterogeneous datasets. External validation on pharmaceutical ingredients, dyes, and supramolecular complexes based on cucurbiturils confirms the reliability of the model. To enhance usability, a script-like tool has been developed, providing a streamlined process for users to access the model. This study represents a significant advancement in pK
$$_a$$
prediction, offering valuable insights for drug design and supramolecular system optimization.
Tài liệu tham khảo
Alcázar JJ, Márquez E, García-Río L et al (2022) Changes in protonation sites of 3-styryl derivatives of 7-(dialkylamino)-aza-coumarin dyes induced by cucurbit[7]uril. Front Chem. https://doi.org/10.3389/fchem.2022.870137
Arrhenius S (1887) Über die Dissociation der in Wasser gelösten Stoffe. Zeitschrift für Physikalische Chemie 1(1):631–648. https://doi.org/10.1515/zpch-1887-0164
Assaf KI, Nau WM (2015) Cucurbiturils: from synthesis to high-affinity binding and catalysis. Chem Soc Rev 44(2):394–418. https://doi.org/10.1039/c4cs00273c
Bajerski L, Rossi RC, Dias CL et al (2010) Development and validation of a discriminating in vitro dissolution method for a poorly soluble drug, Olmesartan Medoxomil: comparison between commercial tablets. AAPS PharmSciTech 11(2):637–644. https://doi.org/10.1208/s12249-010-9421-0
Baldasare CA, Seybold PG (2020) Computational estimation of the gas-phase and aqueous acidities of carbon acids. ACS Appl Mater Interfaces. https://doi.org/10.1021/acs.jpca.9b11964
Baldasare CA, Seybold PG (2021) Computational estimation of the aqueous acidities of alcohols, hydrates, and enols. J Phys Chem A 125(17):3600–3605. https://doi.org/10.1021/acs.jpca.1c01330
Barooah N, Mohanty J, Pal H et al (2012) Stimulus-responsive supramolecular p K a tuning of cucurbit[7]uril encapsulated coumarin 6 dye. J Phys Chem B 116(12):3683–3689. https://doi.org/10.1021/jp212459r
Barooah N, Mohanty J, Pal H et al (2014) Cucurbituril-induced supramolecular pKa shift in fluorescent dyes and its prospective applications. Proc Natl Acad Sci India Sect A Phys Sci 84(1):1–17. https://doi.org/10.1007/s40010-013-0101-9
Barooah N, Sundararajan M, Mohanty J et al (2014) Synergistic effect of intramolecular charge transfer toward supramolecular pKa shift in cucurbit[7]uril encapsulated coumarin dyes. J Phys Chem B 118(25):7136–7146. https://doi.org/10.1021/jp501824p
Barooah N, Mohanty J, Bhasikuttan AC (2022) Cucurbituril-based supramolecular assemblies: prospective on drug delivery, sensing, separation, and catalytic applications. Langmuir. https://doi.org/10.1021/acs.langmuir.2c00556
Berg JM, Tymoczko JL, Gatto GJ et al (2019) Biochemistry, 9th edn. W.H. Freeman and Company, New York
Bernhardsen IM, Knuutila HK (2017) A review of potential amine solvents for CO2 absorption process: absorption capacity, cyclic capacity and pKa. Int J Greenhouse Gas Control 61:27–48. https://doi.org/10.1016/j.ijggc.2017.03.021
Bodnarchuk MS, Heyes DM, Dini D et al (2014) Role of deprotonation free energies in pKa prediction and molecule ranking. J Chem Theory Comput 10(6):2537–2545. https://doi.org/10.1021/ct400914w
Bojesomo RS, Saleh N (2022) Photoinduced electron transfer in encapsulated heterocycles by cavitands. Photochem Photobiol 98(4):754–762. https://doi.org/10.1111/php.13571
Bond T, Templeton MR, Graham N (2012) Precursors of nitrogenous disinfection by-products in drinking water-a critical review and analysis. J Hazard Mater 235–236:1–16. https://doi.org/10.1016/j.jhazmat.2012.07.017
Brandenburg JG, Bannwarth C, Hansen A et al (2018) B97–3c: a revised low-cost variant of the B97-D density functional method. J Chem Phys 148(6):064104. https://doi.org/10.1063/1.5012601
Bredas JL (2014) Mind the gap! Mater Horizons 1(1):17–19. https://doi.org/10.1039/c3mh00098b
Brönsted JN (1934) Zur Theorie der Säuren und Basen und der protolytischen Lösungsmittel. Zeitschrift für Physikalische Chemie 169(1):52–74. https://doi.org/10.1515/zpch-1934-16906
Brönsted JN, Pedersen K (1924) Die katalytische Zersetzung des Nitramids und ihre physikalisch-chemische Bedeutung. Zeitschrift für Physikalische Chemie 108(1):185–235. https://doi.org/10.1515/zpch-1924-10814
Burke K (2012) Perspective on density functional theory. J Chem Phys 136(15):150901. https://doi.org/10.1063/1.4704546
Chandra F, Pal K, Lathwal S et al (2016) Supramolecular guest relay using host-protein nanocavities: an application of host-induced guest protonation. Mol BioSyst 12(9):2859–2866. https://doi.org/10.1039/c6mb00423g
Das B, Baidya AT, Mathew AT et al (2022) Structural modification aimed for improving solubility of lead compounds in early phase drug discovery. Bioorg Med Chem 56:116614. https://doi.org/10.1016/j.bmc.2022.116614
Di Costanzo L, Panunzi B (2021) Visual pH sensors: from a chemical perspective to new bioengineered materials. Molecules 26(10):2952. https://doi.org/10.3390/molecules26102952
Domingo LR (2016) Molecular electron density theory: a modern view of reactivity in organic chemistry. Molecules 21(10):1319. https://doi.org/10.3390/molecules21101319
Dörgő G, Péter Hamadi O, Varga T et al (2020) Mixtures of QSAR models: learning application domains of pKa predicto rs. J Chemometr 34(4):e3223
El-Sheshtawy HS, Chatterjee S, Assaf KI et al (2018) A supramolecular approach for enhanced antibacterial activity and extended shelf-life of fluoroquinolone drugs with cucurbit[7]uril. Sci Rep 8(1):1–10. https://doi.org/10.1038/s41598-018-32312-6
Fujiki R, Matsui T, Shigeta Y et al (2021) Recent developments of computational methods for pKa prediction based on electronic structure theory with solvation models. J 4(4):849–864. https://doi.org/10.3390/j4040058
Funk S, Schatz J (2020) Cucurbiturils in supramolecular catalysis. J Incl Phenomena Macrocyclic Chem 96(1–2):1–27. https://doi.org/10.1007/s10847-019-00956-0
Gaohua L, Miao X, Dou L (2021) Crosstalk of physiological pH and chemical pKa under the umbrella of physiologically based pharmacokinetic modeling of drug absorption, distribution, metabolism, excretion, and toxicity. Expert Opin Drug Metab Toxicol 17(9):1103–1124. https://doi.org/10.1080/17425255.2021.1951223
Geerlings P, De Proft F, Langenaeker W (2003) Conceptual density functional theory. Chem Rev 103(5):1793–1873. https://doi.org/10.1021/cr990029p
Ghosh I, Nau WM (2012) The strategic use of supramolecular pKa shifts to enhance the bioavailability of drugs. Adv Drug Deliv Rev 64(9):764–783. https://doi.org/10.1016/j.addr.2012.01.015
Gramatica P (2020) Principles of QSAR modeling. Int J Quant Struct Prop Relationships 5(3):61–97
Gramatica P, Chirico N, Papa E et al (2013) QSARINS: a new software for the development, analysis, and validation of QSAR MLR models. J Comput Chem 34(24):2121–2132. https://doi.org/10.1002/jcc.23361
Grimme S, Antony J, Ehrlich S et al (2010) A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. J Chem Phys 132(15):154104. https://doi.org/10.1063/1.3382344
Grimme S, Ehrlich S, Goerigk L (2011) Effect of the damping function in dispersion corrected density functional theory. J Comput Chem 32(7):1456–1465. https://doi.org/10.1002/jcc.21759
Gross KC, Seybold PG, Peralta-Inga Z et al (2001) Comparison of quantum chemical parameters and Hammett constants in correlating pKa values of substituted anilines. J Org Chem 66(21):6919–6925. https://doi.org/10.1021/jo010234g
Gu A, Wheate NJ (2021) Macrocycles as drug-enhancing excipients in pharmaceutical formulations. J Incl Phenomena Macrocyclic Chem 100(1–2):55–69. https://doi.org/10.1007/s10847-021-01055-9
Gupta M, Parvathi K, Mula S et al (2017) Enhanced fluorescence of aqueous BODIPY by interaction with cavitand cucurbit[7]uril. Photochem Photobiol Sci 16(4):499–506. https://doi.org/10.1039/C6PP00325G
Haslak ZP, Zareb S, Dogan I et al (2021) Using atomic charges to describe the pKa of carboxylic acids. J Chem Inf Model. https://doi.org/10.1021/acs.jcim.1c00059
Himmel D, Radtke V, Butschke B et al (2018) Basic Remarks on Acidity. Angew Chem Int Ed 57(16):4386–4411. https://doi.org/10.1002/anie.201709057
Holovach S, Melnykov KP, Skreminskiy A et al (2022) Effect of gem-difluorination on the key physicochemical properties relevant to medicinal chemistry: the case of functionalized cycloalkanes. Chem A Eur J 28(19):e202200331. https://doi.org/10.1002/chem.202200331
Holt RA, Seybold PG (2022) Computational estimation of the acidities of pyrimidines and related compounds. Molecules 27(2):385. https://doi.org/10.3390/molecules27020385
Hsieh YL, Ilevbare GA, Van Eerdenbrugh B et al (2012) PH-induced precipitation behavior of weakly basic compounds: determination of extent and duration of supersaturation using potentiometric titration and correlation to solid state properties. Pharm Res 29(10):2738–2753. https://doi.org/10.1007/s11095-012-0759-8
Hunger K (2002) Industrial dyes, 1st edn. Wiley-VCH, Weinheim. https://doi.org/10.1002/3527602011
Juranić I (2014) Simple method for the estimation of pKa of amines. Croatica Chem Acta 87(4):343–347. https://doi.org/10.5562/cca2462
Karelson M, Lobanov VS, Katritzky AR (1996) Quantum-chemical descriptors in QSAR/QSPR studies. Chem Rev 96(3):1027–1043. https://doi.org/10.1021/cr950202r
Kerru N, Gummidi L, Maddila S et al (2020) A review on recent advances in nitrogen-containing molecules and their biological applications. Molecules 25(8):1909. https://doi.org/10.3390/molecules25081909
Khalili F, Rayer AV, Henni A et al (2012) Kinetics and dissociation constants (pKa) of polyamines of importance in post-combustion carbon dioxide (CO2) capture studies. ACS Symp Ser 1097:43–70. https://doi.org/10.1021/bk-2012-1097.ch003
Khurana R, Barooah N, Bhasikuttan AC et al (2017) Modulation in the acidity constant of acridine dye with cucurbiturils: stimuli-responsive pKa tuning and dye relocation into live cells. Org Biomol Chem 15(39):8448–8457. https://doi.org/10.1039/c7ob02135f
Kim MK, Zoh KD (2016) Occurrence and removals of micropollutants in water environment. Environ Eng Res 21(4):319–332. https://doi.org/10.4491/eer.2016.115
Koner AL, Ghosh I, Saleh N et al (2011) Supramolecular encapsulation of benzimidazole-derived drugs by cucurbit[7]uril. Can J Chem 89(2):139–147. https://doi.org/10.1139/V10-079
Kumar A, Singh AK, Singh H et al (2023) Nitrogen containing heterocycles as anticancer agents: a medicinal chemistry perspective. Pharmaceuticals 16(2):299. https://doi.org/10.3390/ph16020299
Lang DK, Kaur R, Arora R et al (2020) Nitrogen-containing heterocycles as anticancer agents: an overview. Anti-Cancer Agents Med Chem 20(18):2150–2168. https://doi.org/10.2174/1871520620666200705214917
Lewis GN (1916) The atom and the molecule. J Am Chem Soc 38(4):762–785. https://doi.org/10.1007/s12045-019-0841-1
Lowry TM (1923) The uniqueness of hydrogen. J Soc Chem Ind 42(3):43–47. https://doi.org/10.1002/jctb.5000420302
Loya JD, Li SJ, Unruh DK et al (2019) Application of the pKa rule to synthesize salts of bezafibrate. Supramol Chem 31(8):558–564. https://doi.org/10.1080/10610278.2019.1635695
Lu T, Chen F (2012) Multiwfn: a multifunctional wavefunction analyzer. J Comput Chem 33(5):580–592. https://doi.org/10.1002/jcc.22885
Lu T, Chen F (2012) Quantitative analysis of molecular surface based on improved Marching Tetrahedra algorithm. J Mol Graph Model 38:314–323. https://doi.org/10.1016/j.jmgm.2012.07.004
Macartney DH (2018) Cucurbit[n]uril host-guest complexes of acids, photoacids, and super photoacids. Israel J Chem 58(3):230–243. https://doi.org/10.1002/ijch.201700096
Manallack DT, Prankerd RJ, Yuriev E et al (2013) The significance of acid/base properties in drug discovery. Chem Soc Rev 42(2):485–496. https://doi.org/10.1039/c2cs35348b
Manjooran G (2020) Pka and ka (Acid dissociation constant). Southern Afr J Anaesth Analgesia 26(6):108. https://doi.org/10.36303/SAJAA.2020.26.6.S3.2552
Marunaka Y (2021) Roles of interstitial fluid pH and weak organic acids in development and amelioration of insulin resistance. Biochem Soc Trans 49(2):715–726. https://doi.org/10.1042/BST20200667
Mendez D, Gaulton A, Bento AP et al (2019) ChEMBL: towards direct deposition of bioassay data. Nucleic Acids Res 47(D1):D930–D940. https://doi.org/10.1093/nar/gky1075
Mohanty J, Barooah N, Bhasikuttan AC (2021) Effect of confinement on the physicochemical properties of chromophoric dyes/drugs with cucurbit[n]uril: prospective applications. Chemical reactivity in confined systems: theory, modelling and applications. John Wiley & Sons, Ltd, pp 371–393. https://doi.org/10.1002/9781119683353.ch19
More KN, Mun SK, Kang J et al (2021) Molecular design of fluorescent pH sensors based on reduced rhodol by structure-pKa relationship for imaging of lysosome. Dyes and pigments 184:108785. https://doi.org/10.1016/j.dyepig.2020.108785
Neese F, Wennmohs F, Becker U et al (2020) The ORCA quantum chemistry program package. J Chem Phys 152(22):224108. https://doi.org/10.1063/5.0004608
O’Neil MJ (2013) The Merck index: an encyclopedia of chemicals, drugs, and biologicals. RSC Publishing
Pahari S, Sun L, Alexov E (2019) PKAD: a database of experimentally measured pKa values of ionizable groups in proteins. Database. https://doi.org/10.1093/database/baz024
Parr RG, Donnelly RA, Levy M et al (1977) Electronegativity: the density functional viewpoint. J Chem Phys 68(8):3801–3807. https://doi.org/10.1063/1.436185
Patel HM, Noolvi MN, Sharma P et al (2014) Quantitative structure–activity relationship (QSAR) studies as strategic approach in drug discovery. Med Chem Res 23(12):4991–5007. https://doi.org/10.1007/s00044-014-1072-3
Politzer P, Murray JS, Bulat FA (2010) Average local ionization energy: a review. J Mol Model 16(11):1731–1742. https://doi.org/10.1007/s00894-010-0709-5
Putz MV, Russo N, Sicilia E (2005) About the Mulliken electronegativity in DFT. Theor Chem Acc 114(1–3):38–45. https://doi.org/10.1007/s00214-005-0641-4
Rebollar-Zepeda AM, Galano A (2012) First principles calculations of pKa values of amines in aqueous solution: application to neurotransmitters. Int J Quant Chem 112(21):3449–3460. https://doi.org/10.1002/qua.24048
Reijenga J, van Hoof A, van Loon A et al (2013) Development of methods for the determination of pKa values. Anal Chem Insights 8(1):53–71. https://doi.org/10.4137/ACI.S12304
Saleh N, Koner AL, Nau WM (2008) Activation and stabilization of drugs by supramolecular pKa shifts: drug-delivery applications tailored for cucurbiturils. Angew Chem Int Ed 47(29):5398–5401. https://doi.org/10.1002/anie.200801054
Sandoval-Lira J, Mondragón-Solórzano G, Lugo-Fuentes LI et al (2020) Accurate estimation of pKb values for amino groups from surface electrostatic potential (VS, min) calculations: the isoelectric points of amino acids as a case study. J Chem Inf Model 60(3):1445–1452. https://doi.org/10.1021/acs.jcim.9b01173
Sashuk V, Butkiewicz H, Fiałkowski M et al (2016) Triggering autocatalytic reaction by host-guest interactions. Chem Commun 52(22):4191–4194. https://doi.org/10.1039/c5cc10063a
Settimo L, Bellman K, Knegtel RM (2014) Comparison of the accuracy of experimental and predicted pKa values of basic and acidic compounds. Pharm Res 31(4):1082–1095. https://doi.org/10.1007/s11095-013-1232-z
Seybold PG (2008) Analysis of the pKas of aliphatic amines using quantum chemical descriptors. Int J Quant Chem 108(15):2849–2855. https://doi.org/10.1002/qua.21809
Seybold PG, Kreye WC (2012) Theoretical estimation of the acidities of alcohols and azoles in gas phase, DMSO, and water. Int J Quant Chem 112(24):3769–3776. https://doi.org/10.1002/qua.24216
Seybold PG, Shields GC (2015) Computational estimation of pKa values. Wiley Interdiscip Rev Comput Mol Sci 5(3):290–297. https://doi.org/10.1002/wcms.1218
Shalaeva M, Kenseth J, Lombardo F et al (2008) Measurement of dissociation constants (pKa values) of organic compounds by multiplexed capillary electrophoresis using aqueous and cosolvent buffers. J Pharm Sci 97(7):2581–2606. https://doi.org/10.1002/jps.21287
Shields GC, Seybold PG (2013) Computational approaches for the prediction of pKa values, 1st edn. CRC Press, Boca Raton. https://doi.org/10.1201/b16128
Silakari O, Singh PK (2021) ADMET tools: prediction and assessment of chemical ADMET properties of NCEs. Concepts and experimental protocols of modelling and informatics in drug design. Elsivier, Amsterdam, pp 299–320. https://doi.org/10.1016/b978-0-12-820546-4.00014-3
Sjoberg P, Murray JS, Brinck T et al (1990) Average local ionization energies on the molecular surfaces of aromatic systems as guides to chemical reactivity. Can J Chem 68(8):1440–1443. https://doi.org/10.1139/v90-220
Soscún Machado HJ, Hinchliffe A (1995) Relationships between the HOMO energies and pKa values in monocyclic and bicyclic azines. J Mol Struct THEOCHEM 339(1–3):255–258. https://doi.org/10.1016/0166-1280(94)04108-5
Sure R, Grimme S (2013) Corrected small basis set Hartree–Fock method for large systems. J Comput Chem 34(19):1672–1685. https://doi.org/10.1002/jcc.23317
Swebocki T, Niedziałkowski P, Cirocka A et al (2020) In pursuit of key features for constructing electrochemical biosensors-electrochemical and acid-base characteristic of self-assembled monolayers on gold. Supramol Chem 32(4):256–266. https://doi.org/10.1080/10610278.2020.1739685
Tam KY, Takács-Novák K (2001) Multi-wavelength spectrophotometric determination of acid dissociation constants: a validation study. Anal Chim Acta 434(1):157–167. https://doi.org/10.1016/S0003-2670(01)00810-8
Tehan BG, Lloyd EJ, Wong MG et al (2002) Estimation of pKa using semiempirical molecular orbital methods. Part 2: application to amines, anilines and various nitrogen containing heterocyclic compounds. Quant Struct Activity Relationships 21(5):473–485. https://doi.org/10.1002/1521-3838(200211)21:5<473::AID-QSAR473>3.0.CO;2-D
Wan H, Holmén AG, Wang Y et al (2003) High-throughput screening of pKa values of pharmaceuticals by pressure-assisted capillary electrophoresis and mass spectrometry. Rapid Commun Mass Spectrometry 17(23):2639–2648. https://doi.org/10.1002/rcm.1229
Wang Z, Sun C, Yang K et al (2022) Cucurbituril-based supramolecular polymers for biomedical applications. Angew Chem 134(38):e202206763. https://doi.org/10.1002/ange.202206763
Watwe V, Kulkarni S, Kulkarni P (2023) Development of dried uncharred leaves of Ficus benjamina as a novel adsorbent for cationic dyes: kinetics, isotherm, and batch optimization. Ind Crops Prod 195:116449. https://doi.org/10.1016/j.indcrop.2023.116449
Yang Q, Li Y, Yang J et al (2020) Holistic prediction of the pKa in diverse solvents based on a machine-learning approach. Angew Chem 132(43):19444–19453. https://doi.org/10.1002/ange.202008528
Yin T, Zhang S, Li M et al (2019) Macrocycle encapsulation triggered supramolecular pKa shift: a fluorescence indicator for detecting octreotide in aqueous solution. Sens Actuat B Chem 281:568–573. https://doi.org/10.1016/j.snb.2018.10.136
Yu H, Kühne R, Ebert RU et al (2010) Comparative analysis of QSAR models for predicting pKa of organic oxygen acids and nitrogen bases from molecular structure. J Chem Inf Model 50(11):1949–1960. https://doi.org/10.1021/ci100306k
Zhang S (2012) A reliable and efficient first principles-based method for predicting pKa values. 4. Organic bases. J Comput Chem 33(31):2469–2482. https://doi.org/10.1002/jcc.23068
Zhang YM, Yang Y, Zhang YH et al (2016) Polysaccharide nanoparticles for efficient siRNA targeting in cancer cells by supramolecular pK a shift. Sci Rep 6(1):1–11. https://doi.org/10.1038/srep28848