1
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Sunsetting Binding MOAD with its last data update and the addition of 3D-ligand polypharmacology tools. Sci Rep 2023; 13:3008. [PMID: 36810894 PMCID: PMC9944886 DOI: 10.1038/s41598-023-29996-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 02/14/2023] [Indexed: 02/24/2023] Open
Abstract
Binding MOAD is a database of protein-ligand complexes and their affinities with many structured relationships across the dataset. The project has been in development for over 20 years, but now, the time has come to bring it to a close. Currently, the database contains 41,409 structures with affinity coverage for 15,223 (37%) complexes. The website BindingMOAD.org provides numerous tools for polypharmacology exploration. Current relationships include links for structures with sequence similarity, 2D ligand similarity, and binding-site similarity. In this last update, we have added 3D ligand similarity using ROCS to identify ligands which may not necessarily be similar in two dimensions but can occupy the same three-dimensional space. For the 20,387 different ligands present in the database, a total of 1,320,511 3D-shape matches between the ligands were added. Examples of the utility of 3D-shape matching in polypharmacology are presented. Finally, plans for future access to the project data are outlined.
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2
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Dutkiewicz Z. Computational methods for calculation of protein-ligand binding affinities in structure-based drug design. PHYSICAL SCIENCES REVIEWS 2022. [DOI: 10.1515/psr-2020-0034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Abstract
Drug design is an expensive and time-consuming process. Any method that allows reducing the time the costs of the drug development project can have great practical value for the pharmaceutical industry. In structure-based drug design, affinity prediction methods are of great importance. The majority of methods used to predict binding free energy in protein-ligand complexes use molecular mechanics methods. However, many limitations of these methods in describing interactions exist. An attempt to go beyond these limits is the application of quantum-mechanical description for all or only part of the analyzed system. However, the extensive use of quantum mechanical (QM) approaches in drug discovery is still a demanding challenge. This chapter briefly reviews selected methods used to calculate protein-ligand binding affinity applied in virtual screening (VS), rescoring of docked poses, and lead optimization stage, including QM methods based on molecular simulations.
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Affiliation(s)
- Zbigniew Dutkiewicz
- Department of Chemical Technology of Drugs , Poznan University of Medical Sciences , ul. Grunwaldzka 6 , 60-780 Poznań , Poznan , 60-780, Poland
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3
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Gu H, Liu L. Molecular modeling and rational design of noncovalent halogen⋯oxygen⋯hydrogen motif at the complex interface of EGFR kinase domain with RALT peptide. Chem Phys 2021. [DOI: 10.1016/j.chemphys.2021.111309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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4
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Zhang A, Liu P, Dou C, Liu Y, Che L. Molecular conversion of MIG6 hotspot-3 peptide from the nonbinder to a moderate binder of HER2 by rational design of an orthogonal interaction system at the HER2-peptide interface. Biophys Chem 2021; 276:106625. [PMID: 34077816 DOI: 10.1016/j.bpc.2021.106625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/15/2021] [Accepted: 05/19/2021] [Indexed: 10/21/2022]
Abstract
Human epidermal growth factor receptor 2 (HER2) has been established as an approved druggable target for the treatment of patients with diverse gynecological tumors such as ovarian, cervical and breast cancers. The mitogen-inducible gene 6 (MIG6) protein is a negative regulator of HER2 signaling by using its Seg1 segment to disrupt the allosteric dimerization of HER2 kinase domain. Previous studies found that the Seg1 adopts three separated hotspots to interact with the HER2 dimerization interface, in which the third hotspot (H3) is located at the core region of the interface but its derived H3 peptide (356PKYVS360) and Tyr358Phe mutant (356PKFVS360) cannot bind effectively to the interface in an independent manner. In this study, we demonstrate that the H3 peptide can be converted from nonbinder to a moderate binder of HER2 by just adding an orthogonal noncovalent interaction system (X⋯O┄H) between a halogen bond (X⋯O) and a hydrogen bond (H┄O) involving peptide Phe358 residue and HER2 Val948/Trp951 residues. High-level calculations are utilized to rigorously characterize and rationally design the X⋯O┄H system, which is then optimized with different halogen atoms and at different substituting positions. It is revealed that there is a synergistic effect between the X⋯O and H┄O of the orthogonal interaction system; formation of the halogen bond can enhance the interaction strength of the hydrogen bond. In silico analysis and in vitro assay reach a consistence that Br-substitution at the m-position of peptide Phe358 phenyl moiety is the best choice that can render strong interaction for the X⋯O┄H system, which also makes the peptide 'bindable' to HER2 kinase domain, while F/Cl/I-substitution at the same position can only improve the peptide affinity moderately or modestly. In contrast, the Br-substitution at the o- and p-positions of peptide Phe358 phenyl moiety cannot define effective X⋯O┄H interaction and thus does not confer additional affinity to the HER2-peptide complex.
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Affiliation(s)
- Aihong Zhang
- Department of Obstetrics and Gynecology, Yidu Central Hospital Affiliated to Weifang Medical University, Weifang 262500, China
| | - Ping Liu
- Department of Obstetrics and Gynecology, Yidu Central Hospital Affiliated to Weifang Medical University, Weifang 262500, China
| | - Chuncheng Dou
- Department of Obstetrics and Gynecology, Yidu Central Hospital Affiliated to Weifang Medical University, Weifang 262500, China
| | - Yao Liu
- Department of Obstetrics and Gynecology, Yidu Central Hospital Affiliated to Weifang Medical University, Weifang 262500, China
| | - Lifan Che
- Department of Obstetrics and Gynecology, Yidu Central Hospital Affiliated to Weifang Medical University, Weifang 262500, China.
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5
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Zhao Y, Zhu D, Gao J. Molecular analysis and systematic profiling of allosteric inhibitor response to clinically significant epidermal growth factor receptor missense mutations in non‐small cell lung cancer. J CHIN CHEM SOC-TAIP 2021. [DOI: 10.1002/jccs.202100217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Yan Zhao
- Department of Cardiothoracic Surgery Zibo First Hospital Zibo China
| | - Dan Zhu
- Shandong Drug and Food Vocational College Weihai China
| | - Junzhen Gao
- Department of Respiratory and Critical Care Medicine Affiliated Hospital of Inner Mongolia Medical University Hohhot China
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6
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Zhang D, He D, Pan X, Liu L. Rational Design and Intramolecular Cyclization of Hotspot Peptide Segments at YAP–TEAD4 Complex Interface. Protein Pept Lett 2020; 27:999-1006. [DOI: 10.2174/0929866527666200414160723] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 02/13/2020] [Accepted: 02/24/2020] [Indexed: 11/22/2022]
Abstract
Background:
The Yes-Associated Protein (YAP) is a central regulator of Hippo pathway
involved in carcinogenesis, which functions through interaction with TEA Domain (TEAD)
transcription factors. Pharmacological disruption of YAP–TEAD4 complexes has been recognized
as a potential therapeutic strategy against diverse cancers by suppressing the oncogenic activity of
YAP.
Objective:
Two peptides, termed PS-1 and PS-2 are split from the interfacial context of YAP protein.
Dynamics simulations, energetics analyses and fluorescence polarizations are employed to
characterize the intrinsic disorder as well as binding energy/affinity of the two YAP peptides to
TEAD4 protein.
Methods:
Two peptides, termed PS-1 and PS-2 are split from the interfacial context of YAP protein.
Dynamics simulations, energetics analyses and fluorescence polarizations are employed to
characterize the intrinsic disorder as well as binding energy/affinity of the two YAP peptides to
TEAD4 protein.
Result:
The native conformation of PS-2 peptide is a cyclic loop, which is supposed to be constrained
by adding a disulfide bond across the spatially vicinal residue pair Arg87-Phe96 or Met86-
Phe95 at the peptide’s two ends, consequently resulting in two intramolecular cyclized counterparts
of linear PS-2 peptide, namely PS-2(cyc87,96) and PS-2(cyc86,95). The linear PS-2 peptide
is determined as a weak binder of TEAD4 (Kd = 190 μM), while the two cyclic PS-2(cyc87,96) and
PS-2(cyc86,95) peptides are measured to have moderate or high affinity towards TEAD4 (Kd = 21
and 45 μM, respectively).
Conclusion:
PS-1 and PS-2 peptides are highly flexible and cannot maintain in native active conformation
when splitting from the interfacial context, and thus would incur a considerable entropy
penalty upon rebinding to the interface. Cyclization does not influence the direct interaction between
PS-2 peptide and TEAD4 protein, but can largely reduce the intrinsic disorder of PS-2 peptide
in free state and considerably minimize indirect entropy effect upon the peptide binding.
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Affiliation(s)
- Dingwa Zhang
- School of Chemistry and Chemical Engineering, Jinggangshan University, Ji’an 343009, China
| | - Deyong He
- School of Chemistry and Chemical Engineering, Jinggangshan University, Ji’an 343009, China
| | - Xiaoliang Pan
- School of Mechanical and Electrical Engineering, Jinggangshan University, Ji’an 343009, China
| | - Lijun Liu
- School of Chemistry and Chemical Engineering, Jinggangshan University, Ji’an 343009, China
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7
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Baek I, Choi H, Yoon S, Na S. Effects of the Hydrophobicity of Key Residues on the Characteristics and Stability of Glucose Oxidase on a Graphene Surface. ACS Biomater Sci Eng 2020; 6:1899-1908. [PMID: 33455332 DOI: 10.1021/acsbiomaterials.9b01763] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Glucose oxidase (GOx) is one of the most widely investigated enzymes in the field of bioelectrochemistry. It is mainly used for the detection of glucose in solutions and enzyme-based biofuel cells. On the basis of the combination of GOx with graphene, novel nanodevices exceeding conventional limits can be developed. To develop a hybrid enzyme-graphene nanodevice with a good performance, it is important that GOx is deposited well on the graphene surface while maintaining its structure and not impeding the oxidation activity of the GOx. In this study, we propose a method to improve the stability of GOx and secure its immobility on the graphene sheet and its glucose-binding affinity by single-point mutation of GOx using molecular dynamics simulations. We confirm that the structural stability, immobility, and substrate binding affinity of GOx can be modified by changing the hydrophobicity of a key residue. We demonstrate that biosensors or biofuel cells can be redesigned and their properties can be improved by using molecular dynamics simulation.
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Affiliation(s)
- Inchul Baek
- Department of Mechanical Engineering Korea University, Seoul 02481, Republic of Korea
| | - Hyunsung Choi
- Department of Mechanical Engineering Korea University, Seoul 02481, Republic of Korea
| | - Seongho Yoon
- College of Engineering Korea University, Seoul 02481, Republic of Korea
| | - Sungsoo Na
- Department of Mechanical Engineering Korea University, Seoul 02481, Republic of Korea
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8
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Second-generation 4,5,6,7-tetrahydrobenzo[ d]thiazoles as novel DNA gyrase inhibitors. Future Med Chem 2020; 12:277-297. [PMID: 32043377 DOI: 10.4155/fmc-2019-0127] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Aim: DNA gyrase and topoisomerase IV are essential bacterial enzymes, and in the fight against bacterial resistance, they are important targets for the development of novel antibacterial drugs. Results: Building from our first generation of 4,5,6,7-tetrahydrobenzo[d]thiazole-based DNA gyrase inhibitors, we designed and prepared an optimized series of analogs that show improved inhibition of DNA gyrase and topoisomerase IV from Staphylococcus aureus and Escherichia coli, with IC50 values in the nanomolar range. Importantly, these inhibitors also show improved antibacterial activity against Gram-positive strains. Conclusion: The most promising inhibitor, 29, is active against Enterococcus faecalis, Enterococcus faecium and S. aureus wild-type and resistant strains, with minimum inhibitory concentrations between 4 and 8 μg/ml, which represents good starting point for development of novel antibacterials.
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9
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Chalopin Y, Piazza F, Mayboroda S, Weisbuch C, Filoche M. Universality of fold-encoded localized vibrations in enzymes. Sci Rep 2019; 9:12835. [PMID: 31492876 PMCID: PMC6731342 DOI: 10.1038/s41598-019-48905-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 08/07/2019] [Indexed: 02/06/2023] Open
Abstract
Enzymes speed up biochemical reactions at the core of life by as much as 15 orders of magnitude. Yet, despite considerable advances, the fine dynamical determinants at the microscopic level of their catalytic proficiency are still elusive. In this work, we use a powerful mathematical approach to show that rate-promoting vibrations in the picosecond range, specifically encoded in the 3D protein structure, are localized vibrations optimally coupled to the chemical reaction coordinates at the active site. Remarkably, our theory also exposes an hithertho unknown deep connection between the unique localization fingerprint and a distinct partition of the 3D fold into independent, foldspanning subdomains that govern long-range communication. The universality of these features is demonstrated on a pool of more than 900 enzyme structures, comprising a total of more than 10,000 experimentally annotated catalytic sites. Our theory provides a unified microscopic rationale for the subtle structure-dynamics-function link in proteins.
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Affiliation(s)
- Yann Chalopin
- Laboratoire d'Energétique Macroscopique et Moléculaire, Combustion (EM2C), CentraleSupélec, CNRS, 91190, Gif-sur-Yvette, France.
| | - Francesco Piazza
- Centre de Biophysique Moléculaire (CBM) CNRS UPR4301 & Université d'Orléans, Orléans, 45071, France
| | - Svitlana Mayboroda
- School of Mathematics, University of Minnesota, Minneapolis, Minnesota, 55455, USA
| | - Claude Weisbuch
- Laboratoire de Physique de la Matière Condensée, Ecole Polytechnique, CNRS, 91128, Palaiseau, France.,Materials Department, University of California, Santa Barbara, California, 93106, USA
| | - Marcel Filoche
- Laboratoire de Physique de la Matière Condensée, Ecole Polytechnique, CNRS, 91128, Palaiseau, France
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10
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Zhang D, He D, Pan X, Xu Y, Liu L. Structural analysis and rational design of orthogonal stacking system in an E. coli DegP PDZ1–peptide complex. CHEMICAL PAPERS 2019. [DOI: 10.1007/s11696-019-00797-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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11
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Sun Z, Liu Q, Qu G, Feng Y, Reetz MT. Utility of B-Factors in Protein Science: Interpreting Rigidity, Flexibility, and Internal Motion and Engineering Thermostability. Chem Rev 2019; 119:1626-1665. [PMID: 30698416 DOI: 10.1021/acs.chemrev.8b00290] [Citation(s) in RCA: 292] [Impact Index Per Article: 58.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Qian Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ge Qu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Manfred T. Reetz
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Chemistry Department, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
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12
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Lv Y, Li J, Fang J, Jiao X, Yan L, Shan B. Systematic profiling of substrate binding response to multidrug-resistant mutations in HIV-1 protease: Implication for combating drug resistance. J Mol Graph Model 2017; 74:83-88. [PMID: 28371730 DOI: 10.1016/j.jmgm.2017.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 03/15/2017] [Accepted: 03/16/2017] [Indexed: 11/30/2022]
Abstract
Human immunodeficiency virus 1 (HIV-1) protease (PR) represents one of the primary targets for developing antiviral agents for the treatment of HIV-infected patients. However, a number of multidrug-resistant mutations in the enzyme have been observed over the past decades, largely limiting the application of PR inhibitors in antiviral therapy. A systematic investigation of the intermolecular interaction between the multidrug-resistant mutants of HIV-1 PR and its substrates would help to establish a complete profile of substrate response to PR mutations and to design new antiviral agents combating drug resistance. Here, we describe an integrative method to profile 6 clinical multidrug-resistant PR mutants against a panel of 16 substrate octapeptides that flank 12 distinct PR cleavage sites in viral precursor polyproteins. It is found that most multidrug-resistant mutations have only a modest or moderate effect on substrate peptide binding, although these mutations would cause a large free energy loss in PR inhibitor binding. Structural analysis reveals that the substrate peptides are loosely bound within PR active pocket to form a wide contact interface between them, and thus mutation of just single or few residues seems not to influence PR-substrate binding considerably. In addition, peptides derived from variable cleavage sites are generally more sensitive to the mutations as compared to those derived from conserved sites, supporting the co-evaluation mechanism of HIV-1 PR and its substrates under drug suppression. We also identify 12 functionally conserved key residues around the enzyme's active site, which play crucial role in substrate recognition. In vitro fluorescence anisotropy assays confirm that wild-type PR can bind substrate peptides ARVL/AEAM and NLAF/PQGE with a moderately high affinity (KD=2 and 16μM, respectively). In contrast, the key residue mutations N25D/D29N can completely eliminate (KD=n.d.) or largely reduce (KD=32 and 120μM, respectively) the binding capability of the two peptides, suggesting that these PR residues could be the potential target sites for developing resistance-free anti-HIV agents.
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Affiliation(s)
- Yonglei Lv
- Henan Red Cross Blood Center, Zhengzhou 450053, PR China
| | - Jianbing Li
- Henan Red Cross Blood Center, Zhengzhou 450053, PR China
| | - Jianhua Fang
- Henan Red Cross Blood Center, Zhengzhou 450053, PR China
| | - Xiufeng Jiao
- Henan Red Cross Blood Center, Zhengzhou 450053, PR China.
| | - Lumin Yan
- Henan Red Cross Blood Center, Zhengzhou 450053, PR China
| | - Baifeng Shan
- Shanxi Provincial Blood Center, Xi'an 710061, PR China
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13
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Qi YJ, Lu HN, Zhao YM, Jin NZ. Probing the influence of carboxyalkyl groups on the molecular flexibility and the charge density of apigenin derivatives. J Mol Model 2017; 23:70. [PMID: 28197841 DOI: 10.1007/s00894-017-3221-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Accepted: 01/11/2017] [Indexed: 12/11/2022]
Abstract
Apigenin is an important flavonoids due to its antidiabetic bioactivity. It was reported experimentally that the 7-substituent derivative of apigenin has higher biological activity than 4'- and 5-substituted derivatives while introducing sole carboxyalkyl group -(CH2)7COOH into the parent structure. Molecular docking studies indicated that the other two derivatives have lower binding affinities than the 7-substituent derivative (-7.52 kcal mol-1), which is considered to be a better inhibitor than the parent molecule. Almost all of the carbon atoms and oxygen atoms are coplaner for all three molecules in solution phase, however, all carboxyalkyl groups bend inside into the parent molecules in the active site, and the jagged geometries of the carbon chains are destroyed correspondingly. In addition, most of the electron densities of the chemical bonds for all molecules are decreased, especially the 7-substituent derivative. In contrast, most of the Laplacian values for three molecules are increased in the active site, which suggests that the charge densities at the bond critical point (bcp) are much more depleted than the solution phase. Dipole moments of derivatives are all increased in the active site, suggesting strong intermolecular interactions. After interacting with the S. cerevisiae α-glucosidase, only the 7-substituent derivative has the lowest energy gap ΔE HOMO-LUMO, which indicates the lowest stability and the highest inhibition activity. Graphical abstract Probing the influence of carboxyalkyl groups on the molecular flexibility and the charge density of apigenin derivatives.
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Affiliation(s)
- Y J Qi
- Department of Chemical Engineering, Northwest University for Nationalities, Lanzhou, 730124, People's Republic of China.
| | - H N Lu
- Department of Life Sciences and Biological Engineering, Northwest University for Nationalities, Lanzhou, 730124, People's Republic of China
| | - Y M Zhao
- Department of Chemical Engineering, Northwest University for Nationalities, Lanzhou, 730124, People's Republic of China
| | - N Z Jin
- Gansu Province Computing Center, Lanzhou, 730000, People's Republic of China
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14
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He D, Huang L, Xu Y, Pan X, Liu L. Computational analysis and enzyme assay of inhibitor response to disease single nucleotide polymorphisms (SNPs) in lipoprotein lipase. J Bioinform Comput Biol 2016; 14:1650028. [DOI: 10.1142/s0219720016500281] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Lipoprotein lipase (LPL) is the rate-limiting enzyme for the hydrolysis of the triglyceride (TG) core of circulating TG-rich lipoproteins, chylomicrons, and very low-density lipoproteins. The enzyme has been established as an efficacious and safe therapeutic target for the management of obesity. Here, a systematic profile of the lipase inhibitor response of three anti-obesity agents (Orlistat, Lipstatin, and Cetilistat) to clinical LPL missense mutations arising from disease single nucleotide polymorphisms (SNPs) was established by integrating complex structure modeling, virtual mutagenesis, molecular dynamics (MD) simulations, binding energy analysis, and radiolabeled TG hydrolysis assays. The profile was then used to characterize the resistance and sensitivity of systematic mutation–inhibitor pairs. It is suggested that the Orlistat and Lipstatin have a similar response profile to the investigated mutations due to their homologous chemical structures, but exhibit a distinct profile to that of Cetilistat. Most mutations were predicted to have a modest or moderate effect on inhibitor binding; they are located far away from the enzyme active site and thus can only influence the binding limitedly. A number of mutations were found to sensitize or cause resistance for lipase inhibitors by directly interacting with the inhibitor ligands or by indirectly addressing allosteric effect on enzyme active site. Long-term MD simulations revealed a different noncovalent interaction network at the complex interfaces of Orlistat with wild-type LPL as well as its sensitized mutant H163R and resistant mutant I221T.
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Affiliation(s)
- Deyong He
- School of Chemistry and Chemical Engineering, Jinggangshan, University, No. 28 Xueyuan Road, Ji’an 343009, China
| | - Ling Huang
- School of Chemistry and Chemical Engineering, Jinggangshan, University, No. 28 Xueyuan Road, Ji’an 343009, China
| | - Yaping Xu
- School of Chemistry and Chemical Engineering, Jinggangshan, University, No. 28 Xueyuan Road, Ji’an 343009, China
| | - Xiaoliang Pan
- School of Mechanical Engineering, Jinggangshan University, No.28 Xueyuan Road, Ji’an 343009, China
| | - Lijun Liu
- School of Chemistry and Chemical Engineering, Jinggangshan, University, No. 28 Xueyuan Road, Ji’an 343009, China
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15
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Exploring molecular flexibility and the interactions of Quercetin derivatives in the active site of α-glucosidase using molecular docking and charge density analysis. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2016.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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16
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Ryde U, Söderhjelm P. Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods. Chem Rev 2016; 116:5520-66. [DOI: 10.1021/acs.chemrev.5b00630] [Citation(s) in RCA: 175] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ulf Ryde
- Department of Theoretical
Chemistry and ‡Department of Biophysical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Pär Söderhjelm
- Department of Theoretical
Chemistry and ‡Department of Biophysical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
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17
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Dou SF, Liu H, Cao TM, Wen QL, Li J, Shao QC. Structure-Based Design of a Br Halogen Bond at the Complex Interface of the Human Placental HtrA1 PDZ Domain with Its Heptapeptide Ligand. Arch Pharm (Weinheim) 2016; 349:302-7. [PMID: 26972470 DOI: 10.1002/ardp.201500466] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Revised: 02/19/2016] [Accepted: 02/23/2016] [Indexed: 11/06/2022]
Abstract
The shock-induced serine protease HtrA1 is a potential regulator of human placenta development during pregnancy. The protein contains a functional PDZ domain that has been solved in complex with a phage display-derived heptapeptide: Asp-6 Ser-5 Arg-4 Ile-3 Trp-2 Trp-1 Val0 . In this study, a rationally designed halogen bond was introduced to the domain-peptide complex based on its NMR structure in solution. We computationally compared the stabilization energies and hindrance effects due to the presence of different halogens X (X = F, Cl, Br, or I), using a hybrid quantum mechanics/molecular mechanics (QM/MM) approach, and found that the Br atom could considerably promote the peptide binding free energy (ΔΔG = -5.2 kcal/mol). Fluorescence assays confirmed that the peptide affinity to the HtrA1 PDZ domain was improved by approximately sevenfold upon bromination. Structural analysis identified a geometrically perfect halogen bond between the Br atom of the peptide Trp-1 residue and the carbonyl O atom of the HtrA1 Ile385 residue, with a bond length and an interaction energy of d = 3.20 Å and ΔE = -3.7 kcal/mol, respectively.
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Affiliation(s)
- Shuo-Fen Dou
- Catheter Room, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Hong Liu
- Department of Obstetrics, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Tong-Mei Cao
- Department of Obstetrics, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Qing-Li Wen
- Department of Obstetrics, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Jie Li
- Department of Obstetrics, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Qing-Chun Shao
- Department of Obstetrics, Affiliated Hospital of Weifang Medical University, Weifang, China
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Liu H, Dou SF, Zhang X, Wang Y, Wen QL, Mu YN. Rational Improvement of Peptide Affinity to Human Pregnancy-Related Serine Protease HtrA3 PDZ Domain by Introducing a Halogen Bond to the Domain–Peptide Complex Interface. Int J Pept Res Ther 2016. [DOI: 10.1007/s10989-016-9516-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Zang P, Gong A, Zhang P, Yu J. Targeting druggable enzymome by exploiting natural medicines: An in silico-in vitro integrated approach to combating multidrug resistance in bacterial infection. PHARMACEUTICAL BIOLOGY 2015; 54:604-618. [PMID: 26681298 DOI: 10.3109/13880209.2015.1068338] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
CONTEXT Antibiotic resistance is a major clinical and public health problem. Development of new therapeutic approaches to prevent bacterial multidrug resistance during antimicrobial chemotherapy has thus been becoming a primary consideration in the medicinal chemistry community. OBJECTIVE We described a new strategy that combats multidrug resistance by using natural medicines to target the druggable enzymome (i.e., enzymatic proteome) of Staphylococcus aureus. MATERIALS AND METHODS A pipeline of integrating in silico analysis and in vitro assay was purposed to identify antibacterial agents from a large library of natural products with diverse structures, high drug-likeness, and relatively low flexibility, with which a systematic interactome of 826 natural product candidates with 125 functionally essential S. aureus enzymes was constructed via a high-throughput cross-docking approach. The obtained docking score matrix was then converted into an array of synthetic scores; each corresponds to a natural product candidate. By systematically examining the docking results, a number of highly promising candidates with potent antibacterial activity were suggested. RESULTS Three natural products, i.e., radicicol, jorumycin, and amygdalin, have been determined to possess strong broad-spectrum potency combating both the drug-resistant and drug-sensitive strains (MIC value <10 μg/ml). In addition, some natural products such as tetrandrine, bilobalide, and arbutin exhibited selective inhibition on different strains. DISCUSSION AND CONCLUSION Combined quantum mechanics/molecular mechanics analysis revealed diverse non-bonded interactions across the complex interfaces of newly identified antibacterial agents with their putative targets GyrB ATPase and tyrosyl-tRNA synthetase.
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Affiliation(s)
- Ping Zang
- a Department of Public Health Management , The Affiliated Hospital of Weifang Medical University , Weifang , China
| | - Aijie Gong
- b Department of Central Sterile Supply , Changyi People's Hospital , Changyi , China
| | | | - Jinling Yu
- d Department of Gynaecology , The Affiliated Hospital of Weifang Medical University , Weifang , China
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Aubailly S, Piazza F. Cutoff lensing: predicting catalytic sites in enzymes. Sci Rep 2015; 5:14874. [PMID: 26445900 PMCID: PMC4597221 DOI: 10.1038/srep14874] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 09/10/2015] [Indexed: 01/12/2023] Open
Abstract
Predicting function-related amino acids in proteins with unknown function or unknown allosteric binding sites in drug-targeted proteins is a task of paramount importance in molecular biomedicine. In this paper we introduce a simple, light and computationally inexpensive structure-based method to identify catalytic sites in enzymes. Our method, termed cutoff lensing, is a general procedure consisting in letting the cutoff used to build an elastic network model increase to large values. A validation of our method against a large database of annotated enzymes shows that optimal values of the cutoff exist such that three different structure-based indicators allow one to recover a maximum of the known catalytic sites. Interestingly, we find that the larger the structures the greater the predictive power afforded by our method. Possible ways to combine the three indicators into a single figure of merit and into a specific sequential analysis are suggested and discussed with reference to the classic case of HIV-protease. Our method could be used as a complement to other sequence- and/or structure-based methods to narrow the results of large-scale screenings.
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Affiliation(s)
- Simon Aubailly
- Université d'Orléans, Centre de Biophysique Moléculaire, CNRS-UPR4301, Rue C. Sadron, 45071, Orléans, France
| | - Francesco Piazza
- Université d'Orléans, Centre de Biophysique Moléculaire, CNRS-UPR4301, Rue C. Sadron, 45071, Orléans, France
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Mohanta TK, Arora PK, Mohanta N, Parida P, Bae H. Identification of new members of the MAPK gene family in plants shows diverse conserved domains and novel activation loop variants. BMC Genomics 2015; 16:58. [PMID: 25888265 PMCID: PMC4363184 DOI: 10.1186/s12864-015-1244-7] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 01/15/2015] [Indexed: 11/30/2022] Open
Abstract
Background Mitogen Activated Protein Kinase (MAPK) signaling is of critical importance in plants and other eukaryotic organisms. The MAPK cascade plays an indispensible role in the growth and development of plants, as well as in biotic and abiotic stress responses. The MAPKs are constitute the most downstream module of the three tier MAPK cascade and are phosphorylated by upstream MAP kinase kinases (MAPKK), which are in turn are phosphorylated by MAP kinase kinase kinase (MAPKKK). The MAPKs play pivotal roles in regulation of many cytoplasmic and nuclear substrates, thus regulating several biological processes. Results A total of 589 MAPKs genes were identified from the genome wide analysis of 40 species. The sequence analysis has revealed the presence of several N- and C-terminal conserved domains. The MAPKs were previously believed to be characterized by the presence of TEY/TDY activation loop motifs. The present study showed that, in addition to presence of activation loop TEY/TDY motifs, MAPKs are also contain MEY, TEM, TQM, TRM, TVY, TSY, TEC and TQY activation loop motifs. Phylogenetic analysis of all predicted MAPKs were clustered into six different groups (group A, B, C, D, E and F), and all predicted MAPKs were assigned with specific names based on their orthology based evolutionary relationships with Arabidopsis or Oryza MAPKs. Conclusion We conducted global analysis of the MAPK gene family of plants from lower eukaryotes to higher eukaryotes and analyzed their genomic and evolutionary aspects. Our study showed the presence of several new activation loop motifs and diverse conserved domains in MAPKs. Advance study of newly identified activation loop motifs can provide further information regarding the downstream signaling cascade activated in response to a wide array of stress conditions, as well as plant growth and development. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1244-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tapan Kumar Mohanta
- School of Biotechnology, Yeungnam University, Daehak Gyeongsan, Gyeonsangbook, 712749, Republic of Korea.
| | - Pankaj Kumar Arora
- School of Biotechnology, Yeungnam University, Daehak Gyeongsan, Gyeonsangbook, 712749, Republic of Korea.
| | - Nibedita Mohanta
- Department of Biotechnology, North Orissa University, Sri Ramchandra Vihar, Takatpur, Baripada, Mayurbhanj, Orissa, 757003, India.
| | - Pratap Parida
- Center for Studies in Biotechnology, Dibrugarh University, Dibrugarh, Assam, 786004, India.
| | - Hanhong Bae
- School of Biotechnology, Yeungnam University, Daehak Gyeongsan, Gyeonsangbook, 712749, Republic of Korea.
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Ni Z, Chen H, Qi X, Jin R. Why is Substrate Peptide Binding Unsusceptible to Multidrug-Resistant Mutations in HIV-1 Protease? A Structural and Energetic Analysis. Int J Pept Res Ther 2013. [DOI: 10.1007/s10989-013-9365-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Holló B, Rodić MV, Bera O, Jovičić M, Leovac VM, Tomić ZD, Mészáros Szécsényi K. Cation- and/or anion-directed reaction routes. Could the desolvation pattern of isostructural coordination compounds be related to their molecular structure? Struct Chem 2013. [DOI: 10.1007/s11224-013-0270-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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