1
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Niu P, Tao Y, Meng Q, Huang Y, Li S, Ding K, Ma D, Ye Z, Fan M. Discovery of novel macrocyclic derivatives as potent and selective cyclin-dependent kinase 2 inhibitors. Bioorg Med Chem 2024; 104:117711. [PMID: 38583237 DOI: 10.1016/j.bmc.2024.117711] [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: 01/21/2024] [Revised: 03/23/2024] [Accepted: 03/31/2024] [Indexed: 04/09/2024]
Abstract
Cyclin-dependent kinase 2 (CDK2) is a member of CDK family of kinases (CDKs) that regulate the cell cycle. Its inopportune or over-activation leads to uncontrolled cell cycle progression and drives numerous types of cancers, especially ovarian, uterine, gastric cancer, as well as those associated with amplified CCNE1 gene. However, developing selective lead compound as CDK2 inhibitors remains challenging owing to similarities in the ATP pockets among different CDKs. Herein, we described the optimization of compound 1, a novel macrocyclic inhibitor targeting CDK2/5/7/9, aiming to discover more selective and metabolically stable lead compound as CDK2 inhibitor. Molecular dynamic (MD) simulations were performed for compound 1 and 9 to gain insights into the improved selectivity against CDK5. Further optimization efforts led to compound 22, exhibiting excellent CDK2 inhibitory activity, good selectivity over other CDKs and potent cellular effects. Based on these characterizations, we propose that compound 22 holds great promise as a potential lead candidate for drug development.
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Affiliation(s)
- Pengpeng Niu
- Academy of Medical Engineering and Translational Medicine (AMT), Tianjin University, Tianjin 300072, China; Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang 310018, China
| | - Yanxin Tao
- School of Life Sciences, Tianjin University, Tianjin 300072, China; Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang 310018, China
| | - Qingyuan Meng
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang 310018, China; School of Molecular Medicine, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310024, China; Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Yixing Huang
- Department of Otorhinolaryngology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310022, China
| | - Shan Li
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang 310018, China; Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, China
| | - Ke Ding
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 20032, China
| | - Dawei Ma
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 20032, China
| | - Zu Ye
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang 310018, China; Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, China.
| | - Mengyang Fan
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang 310018, China; Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, China.
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2
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Lbadaoui-Darvas M, Garberoglio G, Karadima KS, Cordeiro MNDS, Nenes A, Takahama S. Molecular simulations of interfacial systems: challenges, applications and future perspectives. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1980215] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Affiliation(s)
- Mária Lbadaoui-Darvas
- ENAC/IIE; Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Giovanni Garberoglio
- European Centre for Theoretical Studies in Nuclear Physics and Related Areas (FBK-ECT*), Trento, Italy
- Trento Institute for Fundamental Physics and Applications (TIFPA-INFN), Trento, Italy
| | - Katerina S. Karadima
- Department of Chemical Engineering, University of Patras, Patras, Greece
- Institute of Chemical Engineering Sciences, Foundation for Research and Technology Hellas(FORTH-ICE/HT), Patras, Greece
| | | | - Athanasios Nenes
- ENAC/IIE; Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
- Institute of Chemical Engineering Sciences, Foundation for Research and Technology Hellas(FORTH-ICE/HT), Patras, Greece
| | - Satoshi Takahama
- ENAC/IIE; Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
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3
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Li C, Chen W, Lin X, Zhang S, Wang Y, He X, Ren Y. Molecular dynamics study on the stability of foot-and-mouth disease virus particle in salt solution. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1951262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Chen Li
- State Key Laboratory of Multiphase Complex System, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, People’s Republic of China
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, China
| | - Wei Chen
- State Key Laboratory of Multiphase Complex System, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, People’s Republic of China
- Dalian National Laboratory for Clean Energy, Dalian, People’s Republic of China
| | - Xuan Lin
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Songping Zhang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Yufei Wang
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, China
| | - Xianfeng He
- State Key Laboratory of Multiphase Complex System, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, People’s Republic of China
- School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Ying Ren
- State Key Laboratory of Multiphase Complex System, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, People’s Republic of China
- Innovation Academy of Green Manufacture, Chinese Academy of Sciences, Beijing, People’s Republic of China
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4
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Nassab CN, Arooj M, Shehadi IA, Parambath JBM, Kanan SM, Mohamed AA. Lysozyme and Human Serum Albumin Proteins as Potential Nitric Oxide Cardiovascular Drug Carriers: Theoretical and Experimental Investigation. J Phys Chem B 2021; 125:7750-7762. [PMID: 34232651 DOI: 10.1021/acs.jpcb.1c04614] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nitric oxide-containing drugs present a critical remedy for cardiovascular diseases. Nitroglycerin (NG, O-NO) and S-nitrosoglutathione (SNG, S-NO) are the most common nitric oxide drugs for cardiovascular diseases. Insights regarding the binding affinity of NO drugs with lysozyme and human serum albumin (HSA) proteins and their dissociation mechanism will provide inquisitive information regarding the potential of the proteins as drug carriers. For the first time, the binding interactions and affinities are investigated using molecular docking, conventional molecular dynamics, steered molecular dynamics, and umbrella sampling to explore the ability of both proteins to act as nitric oxide drug carriers. The molecular dynamics simulation results showed higher stability of lysozyme-drug complexes compared to HSA. For lysozyme, cardiovascular drugs were bound in the protein cavity mainly by the electrostatic and hydrogen bond interactions with residues ASP53, GLN58, ILE59, ARG62, TRP64, ASP102, and TRP109. For HSA, key binding residues were ARG410, TYR411, LYS414, ARG485, GLU450, ARG486, and SER489. The free energy profiles produced from umbrella sampling also suggest that lysozyme-drug complexes had better binding affinity than HSA-drug. Binding characteristics of nitric oxide-containing drugs NG and SNG to lysozyme and HSA proteins were studied using fluorescence and UV-vis absorption spectroscopy. The relative change in the fluorescence intensity as a function of drug concentrations was analyzed using Stern-Volmer calculations. This was also confirmed by the change in the UV-vis spectra. Fluorescence quenching results of both proteins with the drugs, based on the binding constant values, demonstrated significantly weak binding affinity to NG and strong binding affinity to SNG. Both computational and experimental studies provided important data for understanding protein-drug interactions and will aid in developing potential drug carrier systems in cardiovascular diseases.
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Affiliation(s)
- Chahlaa N Nassab
- Department of Chemistry, College of Sciences, University of Sharjah, Sharjah 27272, UAE
| | - Mahreen Arooj
- Department of Chemistry, College of Sciences, University of Sharjah, Sharjah 27272, UAE
| | - Ihsan A Shehadi
- Department of Chemistry, College of Sciences, University of Sharjah, Sharjah 27272, UAE
| | - Javad B M Parambath
- Department of Chemistry, College of Sciences, University of Sharjah, Sharjah 27272, UAE
| | - Sofian M Kanan
- Department of Biology, Chemistry and Environmental Sciences, American University of Sharjah, Sharjah 26666, UAE
| | - Ahmed A Mohamed
- Department of Chemistry, College of Sciences, University of Sharjah, Sharjah 27272, UAE
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5
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Alamri MA, Tahir ul Qamar M, Mirza MU, Alqahtani SM, Froeyen M, Chen LL. Discovery of human coronaviruses pan-papain-like protease inhibitors using computational approaches. J Pharm Anal 2020; 10:546-559. [PMID: 32874702 PMCID: PMC7453225 DOI: 10.1016/j.jpha.2020.08.012] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 08/23/2020] [Accepted: 08/24/2020] [Indexed: 12/22/2022] Open
Abstract
The papain-like protease (PLpro) is vital for the replication of coronaviruses (CoVs), as well as for escaping innate-immune responses of the host. Hence, it has emerged as an attractive antiviral drug-target. In this study, computational approaches were employed, mainly the structure-based virtual screening coupled with all-atom molecular dynamics (MD) simulations to computationally identify specific inhibitors of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) PLpro, which can be further developed as potential pan-PLpro based broad-spectrum antiviral drugs. The sequence, structure, and functional conserveness of most deadly human CoVs PLpro were explored, and it was revealed that functionally important catalytic triad residues are well conserved among SARS-CoV, SARS-CoV-2, and middle east respiratory syndrome coronavirus (MERS-CoV). The subsequent screening of a focused protease inhibitors database composed of ∼7,000 compounds resulted in the identification of three candidate compounds, ADM_13083841, LMG_15521745, and SYN_15517940. These three compounds established conserved interactions which were further explored through MD simulations, free energy calculations, and residual energy contribution estimated by MM-PB(GB)SA method. All these compounds showed stable conformation and interacted well with the active residues of SARS-CoV-2 PLpro, and showed consistent interaction profile with SARS-CoV PLpro and MERS-CoV PLpro as well. Conclusively, the reported SARS-CoV-2 PLpro specific compounds could serve as seeds for developing potent pan-PLpro based broad-spectrum antiviral drugs against deadly human coronaviruses. Moreover, the presented information related to binding site residual energy contribution could lead to further optimization of these compounds.
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Affiliation(s)
- Mubarak A. Alamri
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Alkarj, Saudi Arabia
| | | | - Muhammad Usman Mirza
- Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, University of Leuven, B-3000, Leuven, Belgium
| | - Safar M. Alqahtani
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Alkarj, Saudi Arabia
| | - Matheus Froeyen
- Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, University of Leuven, B-3000, Leuven, Belgium
| | - Ling-Ling Chen
- College of Life Science and Technology, Guangxi University, Nanning, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
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6
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Pezzella M, El Hage K, Niesen MJM, Shin S, Willard AP, Meuwly M, Karplus M. Water Dynamics Around Proteins: T- and R-States of Hemoglobin and Melittin. J Phys Chem B 2020; 124:6540-6554. [PMID: 32589026 DOI: 10.1021/acs.jpcb.0c04320] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The water dynamics, as characterized by the local hydrophobicity (LH), is investigated for tetrameric hemoglobin (Hb) and dimeric melittin. For the T0 to R0 transition in Hb, it is found that LH provides additional molecular-level insight into the Perutz mechanism, i.e., the breaking and formation of salt bridges at the α1/β2 and α2/β1 interface is accompanied by changes in LH. For Hb in cubic water boxes with 90 and 120 Å edge length it is observed that following a decrease in LH as a consequence of reduced water density or change of water orientation at the protein/water interface the α/β interfaces are destabilized; this is a hallmark of the Perutz stereochemical model for the T to R transition in Hb. The present work thus provides a dynamical view of the classical structural model relevant to the molecular foundations of Hb function. For dimeric melittin, earlier results by Cheng and Rossky [ Nature 1998, 392, 696-699] are confirmed and interpreted on the basis of LH from simulations in which the protein structure is frozen. For the flexible melittin dimer, the changes in the local hydration can be as much as 30% greater than for the rigid dimer, reflecting the fact that protein and water dynamics are coupled.
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Affiliation(s)
- Marco Pezzella
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Krystel El Hage
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.,SABNP, Université Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Michiel J M Niesen
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States
| | - Sucheol Shin
- Department of Chemistry, University of Texas at Austin, Austin, Texas, United States
| | - Adam P Willard
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Martin Karplus
- Department of Chemistry, Harvard University, Cambridge, Massachusetts, United States.,Laboratoire de Chimie Biophysique, ISIS, Université Louis Pasteur, 67000 Strasbourg, France
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7
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Filipe HAL, Esteves MIM, Henriques CA, Antunes FE. Effect of Protein Flexibility from Coarse-Grained Elastic Network Parameterizations on the Calculation of Free Energy Profiles of Ligand Binding. J Chem Theory Comput 2020; 16:4734-4743. [PMID: 32496775 DOI: 10.1021/acs.jctc.0c00418] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The characterization of the affinity and binding mechanism of specific molecules to a protein active site is scientifically and industrially relevant for many applications. In principle, this information can be obtained using molecular dynamics (MD) simulations by calculating the free energy profile of the process. However, this is a computationally demanding calculation. Currently, coarse-grained (CG) force fields are very well implemented for MD simulations of biomolecular systems. These computationally efficient force fields are a major advantage to the study of large model systems and/or those requiring long simulation times. The Martini model is currently one of the most popular CG force fields for these systems. For the specific case of protein simulations, to correctly maintain the macromolecular three-dimensional structure, the Martini model needs to include an elastic network (EN). In this work, the effect of protein flexibility, as induced by three EN models compatible with the Martini force field, was tested on the calculation of free energy profiles for protein-ligand binding. The EN models used were ElNeDyn, GoMartini, and GEN. The binding of triolein (TOG) and triacetin (TAG) to a lipase protein (thermomyces lanuginosa lipase-TLL) was used as a case study. The results show that inclusion of greater flexibility in the CG parameterization of proteins is of high importance in the calculation of the free energy profiles of protein-ligand systems. However, care must be taken in order to avoid unjustified large protein deformations. In addition, due to molecular flexibility there may be no absolute need for the center of the ligand to reach the center of the protein-binding site. The calculation of the energy profile to a distance of about 0.5 nm from the active site center can be sufficient to differentiate the affinity of different ligands to a protein.
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Affiliation(s)
- Hugo A L Filipe
- Coimbra Chemistry Centre, Dept. of Chemistry, University of Coimbra, Rua Larga, Coimbra 3004-535, Portugal
| | - Margarida I M Esteves
- Coimbra Chemistry Centre, Dept. of Chemistry, University of Coimbra, Rua Larga, Coimbra 3004-535, Portugal
| | - César A Henriques
- EcoXperience, HIESE, Quinta Vale do Espinhal, Penela 3230-343, Portugal
| | - Filipe E Antunes
- Coimbra Chemistry Centre, Dept. of Chemistry, University of Coimbra, Rua Larga, Coimbra 3004-535, Portugal
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8
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Gong Q, Zhang H, Zhang H, Chen C. Calculating the absolute binding free energy of the insulin dimer in an explicit solvent. RSC Adv 2020; 10:790-800. [PMID: 35494470 PMCID: PMC9047981 DOI: 10.1039/c9ra08284k] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 12/23/2019] [Indexed: 12/23/2022] Open
Abstract
Insulin is a significant hormone in the regulation of glucose level in the blood. Its monomers bind to each other to form dimers or hexamers through a complex process. To study the binding of the insulin dimer, we first calculate its absolute binding free energy by the steered molecular dynamics method and the confinement method based on a fictitious thermodynamic cycle. After considering some special correction terms, the final calculated binding free energy at 298 K is −8.97 ± 1.41 kcal mol−1, which is close to the experimental value of −7.2 ± 0.8 kcal mol−1. Furthermore, we discuss the important residue–residue interactions between the insulin monomers, including hydrophobic interactions, π–π interactions and hydrogen bond interactions. The analysis reveals five key residues, VlaB12, TyrB16, PheB24, PheB25, and TyrB26, for the dimerization of the insulin. We also perform MM-PBSA calculations for the wild-type dimer and some mutants and study the roles of the key residues by the change of the binding energy of the insulin dimer. In this paper, we calculate the absolute binding free energy of an insulin dimer by steered MD method. The result of −8.97 kcal mol−1 is close to the experimental value −7.2 kcal mol−1. We also analyze the residue–residue interactions.![]()
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Affiliation(s)
- Qiankun Gong
- Biomolecular Physics and Modeling Group
- School of Physics
- Huazhong University of Science and Technology
- Wuhan 430074
- China
| | - Haomiao Zhang
- Biomolecular Physics and Modeling Group
- School of Physics
- Huazhong University of Science and Technology
- Wuhan 430074
- China
| | - Haozhe Zhang
- Biomolecular Physics and Modeling Group
- School of Physics
- Huazhong University of Science and Technology
- Wuhan 430074
- China
| | - Changjun Chen
- Biomolecular Physics and Modeling Group
- School of Physics
- Huazhong University of Science and Technology
- Wuhan 430074
- China
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9
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Ryberg LA, Sønderby P, Bukrinski JT, Harris P, Peters GHJ. Investigations of Albumin–Insulin Detemir Complexes Using Molecular Dynamics Simulations and Free Energy Calculations. Mol Pharm 2019; 17:132-144. [DOI: 10.1021/acs.molpharmaceut.9b00839] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Line A. Ryberg
- Department of Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Pernille Sønderby
- Department of Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | | | - Pernille Harris
- Department of Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Günther H. J. Peters
- Department of Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
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10
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Exploiting Sparse Statistics for a Sequence-Based Prediction of the Effect of Mutations. ALGORITHMS 2019. [DOI: 10.3390/a12100214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Recent work showed that there is a significant difference between the statistics of amino acid triplets and quadruplets in sequences of folded proteins and randomly generated sequences. These statistics were used to assign a score to each sequence and make a prediction whether a sequence is likely to fold. The present paper extends the statistics to higher multiplets and suggests a way to handle the treatment of multiplets that were not found in the set of folded proteins. In particular, foldability predictions were done along the line of the previous work using pentuplet statistics and a way was found to combine the quadruplet and pentuplets statistics to improve the foldability predictions. A different, simpler, score was defined for hextuplets and heptuplets and were used to predict the direction of stability change of a protein upon mutation. With the best score combination the accuracy of the prediction was 73.4%.
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11
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Brunel F, Lesage de la Haye J, Lansalot M, D’Agosto F. New Insight into Cluster Aggregation Mechanism during Polymerization-Induced Self-Assembly by Molecular Dynamics Simulation. J Phys Chem B 2019; 123:6609-6617. [DOI: 10.1021/acs.jpcb.9b03622] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Fabrice Brunel
- Univ Lyon, Université Claude Bernard Lyon 1, CPE Lyon, CNRS, C2P2, 43 Bvd. du 11 Novembre 1918, F-69616 Villeurbanne, France
| | - Jennifer Lesage de la Haye
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, CNES, ArianeGroup, LHCEP, Bât. Raulin, 2 Rue Victor Grignard, F-69622 Villeurbanne, France
| | - Muriel Lansalot
- Univ Lyon, Université Claude Bernard Lyon 1, CPE Lyon, CNRS, C2P2, 43 Bvd. du 11 Novembre 1918, F-69616 Villeurbanne, France
| | - Franck D’Agosto
- Univ Lyon, Université Claude Bernard Lyon 1, CPE Lyon, CNRS, C2P2, 43 Bvd. du 11 Novembre 1918, F-69616 Villeurbanne, France
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12
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Kairys V, Baranauskiene L, Kazlauskiene M, Matulis D, Kazlauskas E. Binding affinity in drug design: experimental and computational techniques. Expert Opin Drug Discov 2019; 14:755-768. [DOI: 10.1080/17460441.2019.1623202] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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
| | | | - 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
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13
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Brickel S, Meuwly M. Molecular Determinants for Rate Acceleration in the Claisen Rearrangement Reaction. J Phys Chem B 2018; 123:448-456. [DOI: 10.1021/acs.jpcb.8b11059] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Sebastian Brickel
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, Basel CH-4056, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, Basel CH-4056, Switzerland
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