1
|
Abstract
Molecular dynamics (MD) simulations have become increasingly useful in the modern drug development process. In this review, we give a broad overview of the current application possibilities of MD in drug discovery and pharmaceutical development. Starting from the target validation step of the drug development process, we give several examples of how MD studies can give important insights into the dynamics and function of identified drug targets such as sirtuins, RAS proteins, or intrinsically disordered proteins. The role of MD in antibody design is also reviewed. In the lead discovery and lead optimization phases, MD facilitates the evaluation of the binding energetics and kinetics of the ligand-receptor interactions, therefore guiding the choice of the best candidate molecules for further development. The importance of considering the biological lipid bilayer environment in the MD simulations of membrane proteins is also discussed, using G-protein coupled receptors and ion channels as well as the drug-metabolizing cytochrome P450 enzymes as relevant examples. Lastly, we discuss the emerging role of MD simulations in facilitating the pharmaceutical formulation development of drugs and candidate drugs. Specifically, we look at how MD can be used in studying the crystalline and amorphous solids, the stability of amorphous drug or drug-polymer formulations, and drug solubility. Moreover, since nanoparticle drug formulations are of great interest in the field of drug delivery research, different applications of nano-particle simulations are also briefly summarized using multiple recent studies as examples. In the future, the role of MD simulations in facilitating the drug development process is likely to grow substantially with the increasing computer power and advancements in the development of force fields and enhanced MD methodologies.
Collapse
|
2
|
Zhu PJ, Yu ZZ, You QD, Jiang ZY. Myeloid cell leukemin-1 inhibitors: a growing arsenal for cancer therapy. Drug Discov Today 2020; 25:1873-1882. [PMID: 32771436 DOI: 10.1016/j.drudis.2020.07.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 06/12/2020] [Accepted: 07/25/2020] [Indexed: 12/13/2022]
Abstract
B-cell lymphoma-2 (Bcl-2) family proteins, comprising proapoptotic proteins (Bax and Bak), antiapoptotic proteins (Bcl-2, Bcl-XL, Bcl-w, Mcl-1, and A1) and BCL-2 homology domain 3 (BH3)-only proteins (Bid, Noxa, and Puma), have long been identified as pivotal apoptosis regulators. As an antiapoptotic member, myeloid cell leukemin-1 (Mcl-1) can bind with proapoptotic proteins and inhibit apoptosis. Mcl-1 is frequently overexpressed and closely associated with oncogenesis and poor prognosis in several cancers, posing a tremendous obstacle for cancer therapy. Recently, an increasing number of Mcl-1-selective small-molecule inhibitors have entered preclinical studies and advanced into clinical trials. In this review, we briefly introduce the role of Mcl-1 in apoptosis and highlight the recent development of Mcl-1 small-molecule inhibitors.
Collapse
Affiliation(s)
- Peng-Ju Zhu
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Ze-Zhou Yu
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Qi-Dong You
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
| | - Zheng-Yu Jiang
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
| |
Collapse
|
3
|
Predicted Hotspot Residues Involved in Allosteric Signal Transmission in Pro-Apoptotic Peptide-Mcl1 Complexes. Biomolecules 2020; 10:biom10081114. [PMID: 32731448 PMCID: PMC7463671 DOI: 10.3390/biom10081114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/16/2020] [Accepted: 07/24/2020] [Indexed: 11/30/2022] Open
Abstract
Mcl1 is a primary member of the Bcl–2 family—anti–apoptotic proteins (AAP)—that is overexpressed in several cancer pathologies. The apoptotic regulation is mediated through the binding of pro-apoptotic peptides (PAPs) (e.g., Bak and Bid) at the canonical hydrophobic binding groove (CBG) of Mcl1. Although all PAPs form amphipathic α-helices, their amino acid sequences vary to different degree. This sequence variation exhibits a central role in the binding partner selectivity towards different AAPs. Thus, constructing a novel peptide or small organic molecule with the ability to mimic the natural regulatory process of PAP is essential to inhibit various AAPs. Previously reported experimental binding free energies (BFEs) were utilized in the current investigation aimed to understand the mechanistic basis of different PAPs targeted to mMcl1. Molecular dynamics (MD) simulations used to estimate BFEs between mMcl1—PAP complexes using Molecular Mechanics-Generalized Born Solvent Accessible (MMGBSA) approach with multiple parameters. Predicted BFE values showed an excellent agreement with the experiment (R2 = 0.92). The van–der Waals (ΔGvdw) and electrostatic (ΔGele) energy terms found to be the main energy components that drive heterodimerization of mMcl1—PAP complexes. Finally, the dynamic network analysis predicted the allosteric signal transmission pathway involves more favorable energy contributing residues. In total, the results obtained from the current investigation may provide valuable insights for the synthesis of a novel peptide or small organic inhibitor targeting Mcl1.
Collapse
|
4
|
Marimuthu P, Razzokov J, Eshonqulov G. Disruption of conserved polar interactions causes a sequential release of Bim mutants from the canonical binding groove of Mcl1. Int J Biol Macromol 2020; 158:364-374. [PMID: 32376253 DOI: 10.1016/j.ijbiomac.2020.04.243] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/25/2020] [Accepted: 04/27/2020] [Indexed: 12/15/2022]
Abstract
Mcl1 is an important anti-apoptotic member of the Bcl2 family proteins that are upregulated in several cancer malignancies. The canonical binding groove (CBG) located at the surface of Mcl1 exhibits a critical role in binding partners selectively via the BH3-domain of pro-apoptotic Bcl2 family members that trigger the downregulation of Mcl1 function. There are several crystal structures of point-mutated pro-apoptotic Bim peptides in complex with Mcl1. However, the mechanistic effects of such point-mutations towards peptide binding and complex stability still remain unexplored. Here, the effects of the reported point mutations in Bim peptides and their binding mechanisms to Mcl1 were computationally evaluated using atomistic-level steered molecular dynamics (SMD) simulations. A range of external-forces and constant-velocities were applied to the Bim peptides to uncover the mechanistic basis of peptide dissociation from the CBG of Mcl1. Although the peptides showed similarities in their dissociation pathways, the peak rupture forces varied significantly. According to simulations results, the disruption of the conserved polar contacts at the complex interface causes a sequential release of the peptides from the CBG of Mcl1. Overall, the results obtained from the current study may provide valuable insights for the development of novel anti-cancer peptide-inhibitors that can downregulate Mcl1's function.
Collapse
Affiliation(s)
- Parthiban Marimuthu
- Structural Bioinformatics Laboratory (SBL), Biochemistry and Pharmacy, Faculty of Science and Engineering, Åbo Akademi University, FI-20520 Turku, Finland.
| | - Jamoliddin Razzokov
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Gofur Eshonqulov
- Department of Physics, National University of Uzbekistan, 100174 Tashkent, Uzbekistan
| |
Collapse
|
5
|
Ge LN, Yan L, Li C, Cheng K. Bavachinin exhibits antitumor activity against non‑small cell lung cancer by targeting PPARγ. Mol Med Rep 2019; 20:2805-2811. [PMID: 31322235 PMCID: PMC6691202 DOI: 10.3892/mmr.2019.10485] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 06/12/2019] [Indexed: 11/23/2022] Open
Abstract
Bavachinin (BNN), one of the main active ingredients of Psoraleacorylifolia, can activate peroxisome proliferator-activated receptor γ (PPARγ). PPARγ has become a promising therapeutic target in cancer. The aim of the present study was to explore the antitumor effects of BNN in non-small cell lung cancer (NSCLC). Cell Counting Kit-8 and lactate dehydrogenase release assays were performed to measure cell toxicity. Western blotting and immunofluorescence were used to analyze the expression of apoptosis-related factors and PPARγ. The ability of PPARγ to bind to BNN was evaluated by drug affinity responsive target stability (DARTS) and cellular thermal shift assay (CETSA). A reactive oxygen species (ROS) assay kit was used to detect the ROS level. The results revealed that the survival rates and cell viability of A549 cells were reduced by BNN in a dose-dependent manner. The present results also demonstrated that BNN dose-dependently changed the expression of Bcl-2, Bax, caspases-3/9 and PPARγ. In addition, through the cytotoxic and anti-proliferative effects, the apoptosis-related proteins' inhibitive properties of BNN were completely inhibited by the PPARγ antagonists T0070907 and GW9662. The DARTS and CETSA results confirmed the protein binding activity of PPARγ. Furthermore, it was demonstrated that the BNN-induced ROS generation was dependent on PPARγ activation. Taken together, the present study demonstrated that BNN induced the death of A549 cells by activating PPARγ, an effect mediated by the increased ROS level. These results highlighted the potential role of BNN as a chemotherapeutic agent against NSCLC.
Collapse
Affiliation(s)
- Lu-Na Ge
- Shandong Medicinal Biotechnology Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong 250062, P.R. China
| | - Lei Yan
- Department of Chemotherapy, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Shandong Cancer Hospital Affiliated to Shandong University, Jinan, Shandong 250117, P.R. China
| | - Cheng Li
- Department of Chemotherapy, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Shandong Cancer Hospital Affiliated to Shandong University, Jinan, Shandong 250117, P.R. China
| | - Kai Cheng
- Department of Chemotherapy, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Shandong Cancer Hospital Affiliated to Shandong University, Jinan, Shandong 250117, P.R. China
| |
Collapse
|
6
|
Investigating the Molecular Basis of N-Substituted 1-Hydroxy-4-Sulfamoyl-2-Naphthoate Compounds Binding to Mcl1. Processes (Basel) 2019. [DOI: 10.3390/pr7040224] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Myeloid cell leukemia-1 (Mcl1) is an anti–apoptotic protein that has gained considerable attention due to its overexpression activity prevents cell death. Therefore, a potential inhibitor that specifically targets Mcl1 with higher binding affinity is necessary. Recently, a series of N-substituted 1-hydroxy-4-sulfamoyl-2-naphthoate compounds was reported that targets Mcl1, but its binding mechanism remains unexplored. Here, we attempted to explore the molecular mechanism of binding to Mcl1 using advanced computational approaches: pharmacophore-based 3D-QSAR, docking, and MD simulation. The selected pharmacophore—NNRRR—yielded a statistically significant 3D-QSAR model containing high confidence scores (R2 = 0.9209, Q2 = 0.8459, and RMSE = 0.3473). The contour maps—comprising hydrogen bond donor, hydrophobic, negative ionic and electron withdrawal effects—from our 3D-QSAR model identified the favorable regions crucial for maximum activity. Furthermore, the external validation of the selected model using enrichment and decoys analysis reveals a high predictive power. Also, the screening capacity of the selected model had scores of 0.94, 0.90, and 8.26 from ROC, AUC, and RIE analysis, respectively. The molecular docking of the highly active compound—C40; 4-(N-benzyl-N-(4-(4-chloro-3,5-dimethylphenoxy) phenyl) sulfamoyl)-1-hydroxy-2-naphthoate—predicted the low-energy conformational pose, and the MD simulation revealed crucial details responsible for the molecular mechanism of binding with Mcl1.
Collapse
|
7
|
Semenyuk P, Muronetz V. Protein Interaction with Charged Macromolecules: From Model Polymers to Unfolded Proteins and Post-Translational Modifications. Int J Mol Sci 2019; 20:E1252. [PMID: 30871103 PMCID: PMC6429204 DOI: 10.3390/ijms20051252] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/05/2019] [Accepted: 03/07/2019] [Indexed: 12/18/2022] Open
Abstract
Interaction of proteins with charged macromolecules is involved in many processes in cells. Firstly, there are many naturally occurred charged polymers such as DNA and RNA, polyphosphates, sulfated glycosaminoglycans, etc., as well as pronouncedly charged proteins such as histones or actin. Electrostatic interactions are also important for "generic" proteins, which are not generally considered as polyanions or polycations. Finally, protein behavior can be altered due to post-translational modifications such as phosphorylation, sulfation, and glycation, which change a local charge of the protein region. Herein we review molecular modeling for the investigation of such interactions, from model polyanions and polycations to unfolded proteins. We will show that electrostatic interactions are ubiquitous, and molecular dynamics simulations provide an outstanding opportunity to look inside binding and reveal the contribution of electrostatic interactions. Since a molecular dynamics simulation is only a model, we will comprehensively consider its relationship with the experimental data.
Collapse
Affiliation(s)
- Pavel Semenyuk
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia.
| | - Vladimir Muronetz
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia.
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia.
| |
Collapse
|
8
|
Xu H, Tang Z, Zuo Y, Xiong F, Chen K, Jiang H, Luo C, Zhang H. Molecular dynamics simulation revealed the intrinsic conformational change of cellular inhibitor of apoptosis protein-1. J Biomol Struct Dyn 2019; 38:975-984. [PMID: 30843765 DOI: 10.1080/07391102.2019.1591303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Inhibitor of apoptosis proteins (IAPs) are important regulators of apoptosis, and protein targets for the development of anti-cancer drugs. Cellular inhibitor of apoptosis protein-1 (cIAP1) is an important member of IAPs. Peptides or small-molecular antagonists can induce the dimerization, auto-ubiquitination, and proteasomal degradation of the cellular inhibitor of apoptosis protein-1 (cIAP1). While in the absence of antagonists, several mutations of the cIAP1 protein also lead to its dimerization and auto-ubiquitination. Even though the crystal structure of cIAP1 protein has been determined, the intrinsic mechanism of its dimerization remains unexplored. Accumulating evidence indicated that intrinsic conformational change existed during the binding of antagonists with cIAP1 protein, or introduction of mutations. To reveal this intrinsic conformational change, molecular dynamics simulations at microsecond scale were applied for the wild-type and mutant-type cIAP1 proteins. Compared to the crystal structure, significant conformational change was observed during the simulations, which could explain the importance of previously identified key mutations. To validate these findings revealed by our simulations, a new mutation D303A was constructed and the following native polyacrylamide gel electrophoresis (native-PAGE) assay observed a proportion of spontaneous dimerization, in comparison with the wild-type control. Taken together, these computational and experimental results revealed the intrinsic conformational change of cIAP1, which could not only explain previously identified key mutations, but also be exploited for further design and development of anti-tumor compounds that target the cIAP1 protein.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Heng Xu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | | | - Yu Zuo
- School of Pharmacy, Nanchang University, Nanchang, China
| | - Fengmin Xiong
- School of Pharmacy, Nanchang University, Nanchang, China
| | - Kaixian Chen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hualiang Jiang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Cheng Luo
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hao Zhang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
9
|
Anantram A, Kundaikar H, Degani M, Prabhu A. Molecular dynamic simulations on an inhibitor of anti-apoptotic Bcl-2 proteins for insights into its interaction mechanism for anti-cancer activity. J Biomol Struct Dyn 2018; 37:3109-3121. [DOI: 10.1080/07391102.2018.1508371] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Aarti Anantram
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai, India
| | - Harish Kundaikar
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai, India
| | - Mariam Degani
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai, India
| | - Arati Prabhu
- Dr. Bhanuben Nanavati College of Pharmacy, Mumbai, India
| |
Collapse
|
10
|
Marimuthu P, Singaravelu K. Unraveling the molecular mechanism of benzothiophene and benzofuran scaffold-merged compounds binding to anti-apoptotic Myeloid cell leukemia 1. J Biomol Struct Dyn 2018; 37:1992-2003. [DOI: 10.1080/07391102.2018.1474805] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Parthiban Marimuthu
- Faculty of Science and Engineering, Structural Bioinformatics Laboratory, Biochemistry, Åbo Akademi University, Turku, Finland
| | - Kalaimathy Singaravelu
- Department of Information Technology, Turku Centre for Biotechnology, University of Turku, Turku, Finland
| |
Collapse
|
11
|
In silico approaches to evaluate the molecular properties of organophosphate compounds to inhibit acetylcholinesterase activity in housefly. J Biomol Struct Dyn 2018; 37:307-320. [PMID: 29322868 DOI: 10.1080/07391102.2018.1426046] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Organophosphate compounds (OPC) have become the primary choice as insecticides and are widely used across the world. Additionally, OPCs were also commonly used as a chemical warfare agent that triggers a great challenge to public safety. Exposure of OPCs to human causes immediate excitation of cholinergic neurotransmission through transient elevation of synaptic acetylcholine (ACh) levels and accumulations. Likewise, prolonged exposure of OPCs can affect the processes in immune response, carbohydrate metabolism, cardiovascular toxicity, and several others. Studies revealed that the toxicity of OPCs was provoked by inhibition of acetylcholinesterase (AChE). Therefore, combined in silico approaches - pharmacophore-based 3D-QSAR model; docking and Molecular Dynamics (MD) - were used to assess the precise and comprehensive effects of series of known OP-derived compounds together with its -log LD50 values. The selected five-featured pharmacophore model - AAHHR.61 - displayed the highest correlation (R2 = .9166), cross-validated coefficient (Q2 = .8221), F = 63.2, Pearson-R = .9615 with low RMSE = .2621 values obtained using five component PLS factors. Subsequently, the well-validated model was then used as a 3D query to search novel OPCs using a high-throughput virtual screening technique. Simultaneously, the docking studies predicted the binding pose of the most active OPC in the MdAChE binding pocket. Additionally, the stability of docking was verified using MD simulation. The results revealed that OP22 and predicted lead compounds bound tightly to S315 of MdAChE through potential hydrogen bond interaction over time. Overall, this study might provide valuable insight into binding mode of OPCs and hit compounds to inhibit AChE in housefly.
Collapse
|
12
|
Marimuthu P, Singaravelu K. Prediction of Hot Spots at Myeloid Cell Leukemia-1-Inhibitor Interface Using Energy Estimation and Alanine Scanning Mutagenesis. Biochemistry 2018; 57:1249-1261. [PMID: 29345906 PMCID: PMC6203182 DOI: 10.1021/acs.biochem.7b01048] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
![]()
Myeloid
cell leukemia 1 (Mcl1) is an antiapoptotic protein that
plays central role in apoptosis regulation. Also, Mcl1 has the potency
to resist apoptotic cues resulting in up-regulation and cancer cell
protection. A molecular probe that has the potential to specifically
target Mcl1 and thereby provoke its down-regulatory activity is very
essential. The aim of the current study is to probe the internal conformational
dynamics of protein motions and potential binding mechanism in response
to a series of picomolar range Mcl1 inhibitors using explicit-solvent
molecular dynamics (MD) simulations. Subsequently, domain cross-correlation
and principal component analysis was performed on the snapshots obtained
from the MD simulations. Our results showed significant differences
in the internal conformational dynamics of Mcl1 with respect to binding
affinity values of inhibitors. Further, the binding free energy estimation,
using three different samples, was performed on the MD simulations
and revealed that the predicted energies (ΔGmmgbsa) were in good correlation with the experimental
values (ΔGexpt). Also, the energies
obtained using all sampling models were efficiently ranked. Subsequently,
the decomposition energy analysis highlighted the major energy-contributing
residues at the Mcl1 binding pocket. Computational alanine scanning
performed on high energy-contributing residues predicted the hot spot
residues. The dihedral angle analysis using MD snapshots on the predicted
hot spot residue exhibited consistency in side chain conformational
motion that ultimately led to strong binding affinity values. The
findings from the present study might provide valuable guidelines
for the design of novel Mcl1 inhibitors that might significantly improve
the specificity for new-generation chemotherapeutic agents.
Collapse
Affiliation(s)
- Parthiban Marimuthu
- Structural Bioinformatics Laboratory (SBL), Faculty of Science and Engineering, Biochemistry, Åbo Akademi University , Tykistökatu 6A, FI-20520 Turku, Finland.,Department of Biology, Albany State University , 504 College Dr., Albany, Georgia, United States
| | | |
Collapse
|
13
|
Marimuthu P, Balasubramanian PK, Singaravelu K. Deciphering the crucial molecular properties of a series of Benzothiazole Hydrazone inhibitors that targets anti-apoptotic Bcl-xL protein. J Biomol Struct Dyn 2017; 36:2654-2667. [DOI: 10.1080/07391102.2017.1365771] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Parthiban Marimuthu
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Tykistökatu 6A, Turku FI-20520, Finland
- Department of Biology, Albany State University, 504 College Drive, Albany, GA, USA
| | - Pavithra K. Balasubramanian
- Department of Biomedical Sciences, College of Medicine, Chosun University, 375 Seosuk-dong, Dong-gu, Gwangju 61452, Republic of Korea
| | | |
Collapse
|