1
|
Kairys V, Baranauskiene L, Kazlauskiene M, Zubrienė A, Petrauskas V, Matulis D, Kazlauskas E. Recent advances in computational and experimental protein-ligand affinity determination techniques. Expert Opin Drug Discov 2024; 19:649-670. [PMID: 38715415 DOI: 10.1080/17460441.2024.2349169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 04/25/2024] [Indexed: 05/22/2024]
Abstract
INTRODUCTION Modern drug discovery revolves around designing ligands that target the chosen biomolecule, typically proteins. For this, the evaluation of affinities of putative ligands is crucial. This has given rise to a multitude of dedicated computational and experimental methods that are constantly being developed and improved. AREAS COVERED In this review, the authors reassess both the industry mainstays and the newest trends among the methods for protein - small-molecule affinity determination. They discuss both computational affinity predictions and experimental techniques, describing their basic principles, main limitations, and advantages. Together, this serves as initial guide to the currently most popular and cutting-edge ligand-binding assays employed in rational drug design. EXPERT OPINION The affinity determination methods continue to develop toward miniaturization, high-throughput, and in-cell application. Moreover, the availability of data analysis tools has been constantly increasing. Nevertheless, cross-verification of data using at least two different techniques and careful result interpretation remain of utmost importance.
Collapse
Affiliation(s)
- Visvaldas Kairys
- Department of Bioinformatics, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Lina Baranauskiene
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | | | - Asta Zubrienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Vytautas Petrauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Egidijus Kazlauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| |
Collapse
|
2
|
Renault JP, Huart L, Milosavljević AR, Bozek JD, Palaudoux J, Guigner JM, Marichal L, Leroy J, Wien F, Hervé Du Penhoat MA, Nicolas C. Electronic Structure and Solvation Effects from Core and Valence Photoelectron Spectroscopy of Serum Albumin. Int J Mol Sci 2022; 23:ijms23158227. [PMID: 35897833 PMCID: PMC9331649 DOI: 10.3390/ijms23158227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 12/07/2022] Open
Abstract
X-ray photoelectron spectroscopy of bovine serum albumin (BSA) in a liquid jet is used to investigate the electronic structure of a solvated protein, yielding insight into charge transfer mechanisms in biological systems in their natural environment. No structural damage was observed in BSA following X-ray photoelectron spectroscopy in a liquid jet sample environment. Carbon and nitrogen atoms in different chemical environments were resolved in the X-ray photoelectron spectra of both solid and solvated BSA. The calculations of charge distributions demonstrate the difficulty of assigning chemical contributions in complex systems in an aqueous environment. The high-resolution X-ray core electron spectra recorded are unchanged upon solvation. A comparison of the valence bands of BSA in both phases is also presented. These bands display a higher sensitivity to solvation effects. The ionization energy of the solvated BSA is determined at 5.7 ± 0.3 eV. Experimental results are compared with theoretical calculations to distinguish the contributions of various molecular components to the electronic structure. This comparison points towards the role of water in hole delocalization in proteins.
Collapse
Affiliation(s)
- Jean-Philippe Renault
- Université Paris-Saclay, CEA, CNRS, NIMBE, CEA Saclay, 91191 Gif-sur-Yvette, France; (L.H.); (L.M.); (J.L.)
- Correspondence: (J.-P.R.); (C.N.)
| | - Lucie Huart
- Université Paris-Saclay, CEA, CNRS, NIMBE, CEA Saclay, 91191 Gif-sur-Yvette, France; (L.H.); (L.M.); (J.L.)
- Synchrotron SOLEIL, 91192 Saint Aubin, France; (A.R.M.); (J.D.B.); (F.W.)
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université, UMR CNRS 7590, MNHN, 75252 Paris, France; (J.-M.G.); (M.-A.H.D.P.)
| | | | - John D. Bozek
- Synchrotron SOLEIL, 91192 Saint Aubin, France; (A.R.M.); (J.D.B.); (F.W.)
| | - Jerôme Palaudoux
- Laboratoire de Chimie Physique-Matière et Rayonnement, Sorbonne Université, UMR CNRS 7614, 75252 Paris, France;
| | - Jean-Michel Guigner
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université, UMR CNRS 7590, MNHN, 75252 Paris, France; (J.-M.G.); (M.-A.H.D.P.)
| | - Laurent Marichal
- Université Paris-Saclay, CEA, CNRS, NIMBE, CEA Saclay, 91191 Gif-sur-Yvette, France; (L.H.); (L.M.); (J.L.)
| | - Jocelyne Leroy
- Université Paris-Saclay, CEA, CNRS, NIMBE, CEA Saclay, 91191 Gif-sur-Yvette, France; (L.H.); (L.M.); (J.L.)
| | - Frank Wien
- Synchrotron SOLEIL, 91192 Saint Aubin, France; (A.R.M.); (J.D.B.); (F.W.)
| | - Marie-Anne Hervé Du Penhoat
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université, UMR CNRS 7590, MNHN, 75252 Paris, France; (J.-M.G.); (M.-A.H.D.P.)
| | - Christophe Nicolas
- Synchrotron SOLEIL, 91192 Saint Aubin, France; (A.R.M.); (J.D.B.); (F.W.)
- Correspondence: (J.-P.R.); (C.N.)
| |
Collapse
|
3
|
Gray M, Herbert JM. Comprehensive Basis-Set Testing of Extended Symmetry-Adapted Perturbation Theory and Assessment of Mixed-Basis Combinations to Reduce Cost. J Chem Theory Comput 2022; 18:2308-2330. [PMID: 35289608 DOI: 10.1021/acs.jctc.1c01302] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Hybrid or "extended" symmetry-adapted perturbation theory (XSAPT) replaces traditional SAPT's treatment of dispersion with better performing alternatives while at the same time extending two-body (dimer) SAPT to a many-body treatment of polarization using a self-consistent charge embedding procedure. The present work presents a systematic study of how XSAPT interaction energies and energy components converge with respect to the choice of Gaussian basis set. Errors can be reduced in a systematic way using correlation-consistent basis sets, with aug-cc-pVTZ results converged within <0.1 kcal/mol. Similar (if slightly less systematic) behavior is obtained using Karlsruhe basis sets at much lower cost, and we introduce new versions with limited augmentation that are even more efficient. Pople-style basis sets, which are more efficient still, often afford good results if a large number of polarization functions are included. The dispersion models used in XSAPT afford much faster basis-set convergence as compared to the perturbative description of dispersion in conventional SAPT, meaning that "compromise" basis sets (such as jun-cc-pVDZ) are no longer required and benchmark-quality results can be obtained using triple-ζ basis sets. The use of diffuse functions proves to be essential, especially for the description of hydrogen bonds. The "δ(Hartree-Fock)" correction for high-order induction can be performed in double-ζ basis sets without significant loss of accuracy, leading to a mixed-basis approach that offers 4× speedup over the existing (cubic scaling) XSAPT approach.
Collapse
Affiliation(s)
- Montgomery Gray
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| |
Collapse
|
4
|
Lidskog A, Dawaigher S, Solano Arribas C, Ryberg A, Jensen J, Bergquist KE, Sundin A, Norrby PO, Wärnmark K. Experimental and Computational Models for Side Chain Discrimination in Peptide-Protein Interactions. Chemistry 2021; 27:10883-10897. [PMID: 33908678 PMCID: PMC8362025 DOI: 10.1002/chem.202100890] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Indexed: 12/02/2022]
Abstract
A bis(18‐crown‐6) Tröger's base receptor and 4‐substituted hepta‐1,7‐diyl bisammonium salt ligands have been used as a model system to study the interactions between non‐polar side chains of peptides and an aromatic cavity of a protein. NMR titrations and NOESY/ROESY NMR spectroscopy were used to analyze the discrimination of the ligands by the receptor based on the substituent of the ligand, both quantitatively (free binding energies) and qualitatively (conformations). The analysis showed that an all‐anti conformation of the heptane chain was preferred for most of the ligands, both free and when bound to the receptor, and that for all of the receptor‐ligand complexes, the substituent was located inside or partly inside of the aromatic cavity of the receptor. We estimated the free binding energy of a methyl‐ and a phenyl group to an aromatic cavity, via CH‐π, and combined aromatic CH‐π and π‐π interactions to be −1.7 and −3.3 kJ mol−1, respectively. The experimental results were used to assess the accuracy of different computational methods, including molecular mechanics (MM) and density functional theory (DFT) methods, showing that MM was superior.
Collapse
Affiliation(s)
- Anna Lidskog
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, P. O Box 124, S-221 00, Lund, Sweden
| | - Sami Dawaigher
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, P. O Box 124, S-221 00, Lund, Sweden
| | - Carlos Solano Arribas
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, P. O Box 124, S-221 00, Lund, Sweden
| | - Anna Ryberg
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, P. O Box 124, S-221 00, Lund, Sweden
| | - Jacob Jensen
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, P. O Box 124, S-221 00, Lund, Sweden
| | - Karl Erik Bergquist
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, P. O Box 124, S-221 00, Lund, Sweden
| | - Anders Sundin
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, P. O Box 124, S-221 00, Lund, Sweden
| | - Per-Ola Norrby
- Data Science & Modelling, Pharmaceutical Sciences, R&D, AstraZeneca Gothenburg, Gothenburg, Sweden
| | - Kenneth Wärnmark
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, P. O Box 124, S-221 00, Lund, Sweden
| |
Collapse
|