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Efimov AV, Meshcheryakova OV, Ryazanov AG. Agonists in the Extended Conformation Stabilize the Active State of β-Adrenoceptors. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:628-639. [PMID: 36154885 DOI: 10.1134/s0006297922070057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/21/2022] [Accepted: 06/21/2022] [Indexed: 06/16/2023]
Abstract
In this study, we conducted a comparative analysis of the structure of agonists and antagonists of transmembrane (TM) β-adrenoceptors (β-ARs) and their interactions with the β-ARs and proposed the mechanism of receptor activation. A characteristic feature of agonist and antagonist molecules is the presence of a hydrophobic head (most often, one or two aromatic rings) and a tail with a positively charged amino group. All β-adrenergic agonists have two carbon atoms between the aromatic ring of the head and the nitrogen atom of the amino group. In antagonist molecules, this fragment can be either reduced or increased to four atoms due to the additional carbon and oxygen atoms. The agonist head, as a rule, has two H-bond donors or acceptors in the para- and meta-positions of the aromatic rings, while in the antagonist heads, these donors/acceptors are absent or located in other positions. Analysis of known three-dimensional structures of β-AR complexes with agonists showed that the agonist head forms two H-bonds with the TM5 helix, and the tail forms an ionic bond with the D3.32 residue of the TM3 helix and one or two H-bonds with the TM7 helix. The tail of the antagonist can form similar bonds, but the interaction between the head and the TM5 helix is much weaker. As a result of these interactions, the agonist molecule acquires an extended "strained string" conformation, in contrast to the antagonist molecule, which has a longer, bended, and flexible tail. The "strained string" of the agonist interacts with the TM6 helix (primarily with the W6.48 residue) and turns it, which leads to the opening of the G protein-binding site on the intracellular side of the receptor, while flexible and larger antagonist molecules do not have the same effect on the receptor.
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Affiliation(s)
- Alexander V Efimov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
| | - Olga V Meshcheryakova
- Institute of Biology of the Karelian Research Centre of the Russian Academy of Sciences, 185910 Petrozavodsk, Russia.
| | - Alexey G Ryazanov
- Department of Pharmacology, Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey, 08854, USA.
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Cruz JN, Costa JFS, Khayat AS, Kuca K, Barros CAL, Neto AMJC. Molecular dynamics simulation and binding free energy studies of novel leads belonging to the benzofuran class inhibitors of Mycobacterium tuberculosis Polyketide Synthase 13. J Biomol Struct Dyn 2018; 37:1616-1627. [PMID: 29633908 DOI: 10.1080/07391102.2018.1462734] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
In this work, the binding mechanism of new Polyketide Synthase 13 (Pks13) inhibitors has been studied through molecular dynamics simulation and free energy calculations. The drug Tam1 and its analogs, belonging to the benzofuran class, were submitted to 100 ns simulations, and according to the results obtained for root mean square deviation, all the simulations converged from approximately 30 ns. For the analysis of backbone flotation, the root mean square fluctuations were plotted for the Cα atoms; analysis revealed that the greatest fluctuation occurred in the residues that are part of the protein lid domain. The binding free energy value (ΔGbind) obtained for the Tam16 lead molecule was of -51.43 kcal/mol. When comparing this result with the ΔGbind values for the remaining analogs, the drug Tam16 was found to be the highest ranked: this result is in agreement with the experimental results obtained by Aggarwal and collaborators, where it was verified that the IC50 for Tam16 is the smallest necessary to inhibit the Pks13 (IC50 = 0.19 μM). The energy decomposition analysis suggested that the residues which most interact with inhibitors are: Ser1636, Tyr1637, Asn1640, Ala1667, Phe1670, and Tyr1674, from which the greatest energy contribution to Phe1670 was particularly notable. For the lead molecule Tam16, a hydrogen bond with the hydroxyl of the phenol not observed in the other analogs induced a more stable molecular structure. Aggarwal and colleagues reported this hydrogen bonding as being responsible for the stability of the molecule, optimizing its physic-chemical, toxicological, and pharmacokinetic properties.
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Key Words
- CNPq, National Council for Scientific and Technological Development
- CoA, coenzyme A
- FAS, fatty acid synthase
- GAFF, general amber force field
- GB, generalized born
- HB, hydrogen bonds
- INH, isoniazid
- KatG, catalase-peroxidase
- MD, molecular dynamics
- MDR, multi-drug resistant
- MM/GBSA, molecular mechanics/generalized-born surface area
- NAD, nicotinamide adenine dinucleotide
- NS, nanoseconds
- PCA, acyl carrier protein
- Pks13
- Pks13, polyketide synthase 13
- RESP, restrained electrostatic potential
- RMSD, root mean square deviation
- RMSF, root mean square fluctuations
- TB, tuberculosis
- TE, C-terminal thioesterase
- XDR, extensively drug resistant
- benzofuran
- free energy
- inhibitors
- molecular dynamics
- Δ internal energy
- Δ, Van Der Waals contributions
- Δ, electrostatic contribution
- Δ, electrostatic contributions
- Δ, energy of desolvation
- Δ, energy of the molecular mechanics
- Δ, non-polar contributions
- Δ, polar contributions
- Δ, polar solvation contribution
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Affiliation(s)
- Jorddy N Cruz
- a Laboratory of Preparation and Computation of Nanomaterials , Federal University of Pará , CP 479, 66075-110 Belém , PA , Brazil
| | - José F S Costa
- a Laboratory of Preparation and Computation of Nanomaterials , Federal University of Pará , CP 479, 66075-110 Belém , PA , Brazil
| | - André S Khayat
- b Oncology Research Center , Federal University of Pará , CP 479, 6675-105 Belém , PA , Brazil
| | - Kamil Kuca
- c Biomedical Research Center , University Hospital Hradec Kralove , Sokolska 581, 500 05 Hradec Kralove , Czech Republic
| | - Carlos A L Barros
- d Department of Pharmacy , Federal University of Pará , CP 479, 66050-160 Belém , PA , Brazil
| | - A M J C Neto
- a Laboratory of Preparation and Computation of Nanomaterials , Federal University of Pará , CP 479, 66075-110 Belém , PA , Brazil
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Iglesias J, Saen‐oon S, Soliva R, Guallar V. Computational structure‐based drug design: Predicting target flexibility. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1367] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
| | | | | | - Victor Guallar
- Life Science DepartmentBarcelonaSpain
- ICREA, Passeig Lluís Companys 23BarcelonaSpain
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Chen K, Duan W, Han Q, Sun X, Li W, Hu S, Wan J, Wu J, Ge Y, Liu D. Identification of the hot spot residues for pyridine derivative inhibitor CCT251455 and ATP substrate binding on monopolar spindle 1 (MPS1) kinase by molecular dynamic simulation. J Biomol Struct Dyn 2018; 37:611-622. [PMID: 29380674 DOI: 10.1080/07391102.2018.1433552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Protein kinase monopolar spindle 1 plays an important role in spindle assembly checkpoint at the onset of mitosis. Over expression of MPS1 correlated with a wide range of human tumors makes it an attractive target for finding an effective and specific inhibitor. In this work, we performed molecular dynamics simulations of protein MPS1 itself as well as protein bound systems with the inhibitor and natural substrate based on crystal structures. The reported orally bioavailable 1 h-pyrrolo [3,2-c] pyridine inhibitors of MPS1 maintained stable binding in the catalytic site, while natural substrate ATP could not stay. Comparative study of stability and flexibility of three systems reveals position shifting of β-sheet region within the catalytic site, which indicates inhibition mechanism was through stabilizing the β-sheet region. Binding free energies calculated with MM-GB/PBSA method shows different binding affinity for inhibitor and ATP. Finally, interactions between protein and inhibitor during molecular dynamic simulations were measured and counted. Residue Gly605 and Leu654 were suggested as important hot spots for stable binding of inhibitor by molecular dynamic simulation. Our results reveal an important position shifting within catalytic site for non-inhibited proteins. Together with hot spots found by molecular dynamic simulation, the results provide important information of inhibition mechanism and will be referenced for designing novel inhibitors.
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Affiliation(s)
- Kai Chen
- a Collaborative Innovation Center of Chemistry for Life Sciences, Institute of Immunology and the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences , University of Sciences and Technology of China , Hefei , 230027 , P. R. China
| | - Wenxiu Duan
- a Collaborative Innovation Center of Chemistry for Life Sciences, Institute of Immunology and the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences , University of Sciences and Technology of China , Hefei , 230027 , P. R. China
| | - Qianqian Han
- a Collaborative Innovation Center of Chemistry for Life Sciences, Institute of Immunology and the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences , University of Sciences and Technology of China , Hefei , 230027 , P. R. China
| | - Xuan Sun
- a Collaborative Innovation Center of Chemistry for Life Sciences, Institute of Immunology and the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences , University of Sciences and Technology of China , Hefei , 230027 , P. R. China
| | - Wenqian Li
- a Collaborative Innovation Center of Chemistry for Life Sciences, Institute of Immunology and the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences , University of Sciences and Technology of China , Hefei , 230027 , P. R. China
| | - Shuangyun Hu
- a Collaborative Innovation Center of Chemistry for Life Sciences, Institute of Immunology and the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences , University of Sciences and Technology of China , Hefei , 230027 , P. R. China
| | - Jiajia Wan
- a Collaborative Innovation Center of Chemistry for Life Sciences, Institute of Immunology and the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences , University of Sciences and Technology of China , Hefei , 230027 , P. R. China
| | - Jiang Wu
- a Collaborative Innovation Center of Chemistry for Life Sciences, Institute of Immunology and the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences , University of Sciences and Technology of China , Hefei , 230027 , P. R. China
| | - Yushu Ge
- a Collaborative Innovation Center of Chemistry for Life Sciences, Institute of Immunology and the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences , University of Sciences and Technology of China , Hefei , 230027 , P. R. China
| | - Dan Liu
- a Collaborative Innovation Center of Chemistry for Life Sciences, Institute of Immunology and the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences , University of Sciences and Technology of China , Hefei , 230027 , P. R. China
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