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Reddy CN, Sankararamakrishnan R. Molecular dynamics studies of CED-4/CED-9/EGL-1 ternary complex reveal CED-4 release mechanism in the linear apoptotic pathway of Caenorhabditis elegans. Proteins 2022; 91:679-693. [PMID: 36541866 DOI: 10.1002/prot.26457] [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: 07/06/2022] [Revised: 11/14/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022]
Abstract
Many steps in programmed cell death are evolutionarily conserved across different species. The Caenorhabditis elegans proteins CED-9, CED-4 and EGL-1 involved in apoptosis are respectively homologous to anti-apoptotic Bcl-2 proteins, Apaf-1 and the "BH3-only" pro-apototic proteins in mammals. In the linear apoptotic pathway of C. elegans, EGL-1 binding to CED-9 leads to the release of CED-4 from CED-9/CED-4 complex. The molecular events leading to this process are not clearly elucidated. While the structures of CED-9 apo, CED-9/EGL-1 and CED-9/CED-4 complexes are known, the CED-9/CED-4/EGL-1 ternary complex structure is not yet determined. In this work, we modeled this ternary complex and performed molecular dynamics simulations of six different systems involving CED-9. CED-9 displays differential dynamics depending upon whether it is bound to CED-4 and/or EGL-1. CED-4 exists as an asymmetric dimer (CED4a and CED4b) in CED-9/CED-4 complex. CED-4a exhibits higher conformational flexibility when simulated without CED-4b. Principal Component Analysis revealed that the direction of CED-4a's winged-helix domain motion differs in the ternary complex. Upon EGL-1 binding, majority of non-covalent interactions involving CARD domain in the CED-4a-CED-9 interface have weakened and only half of the contacts found in the crystal structure between α/β domain of CED4a and CED-9 are found to be stable. Additional stable contacts in the ternary complex and differential dynamics indicate that winged-helix domain may play a key role in CED-4a's dissociation from CED-9. This study has provided a molecular level understanding of potential intermediate states that are likely to occur when CED-4a is released from CED-9.
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Affiliation(s)
- C Narendra Reddy
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, India
| | - Ramasubbu Sankararamakrishnan
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, India.,Mehta Family Centre for Engineering in Medicine, Indian Institute of Technology Kanpur, Kanpur, India
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Reddy CN, Manzar N, Ateeq B, Sankararamakrishnan R. Computational Design of BH3-Mimetic Peptide Inhibitors That Can Bind Specifically to Mcl-1 or Bcl-X L: Role of Non-Hot Spot Residues. Biochemistry 2020; 59:4379-4394. [PMID: 33146015 DOI: 10.1021/acs.biochem.0c00661] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Interactions between pro- and anti-apoptotic Bcl-2 proteins decide the fate of the cell. The BH3 domain of pro-apoptotic Bcl-2 proteins interacts with the exposed hydrophobic groove of their anti-apoptotic counterparts. Through their design and development, BH3 mimetics that target the hydrophobic groove of specific anti-apoptotic Bcl-2 proteins have the potential to become anticancer drugs. We have developed a novel computational method for designing sequences with BH3 domain features that can bind specifically to anti-apoptotic Mcl-1 or Bcl-XL. In this method, we retained the four highly conserved hydrophobic and aspartic residues of wild-type BH3 sequences and randomly substituted all other positions to generate a large number of BH3-like sequences. We modeled 20000 complex structures with Mcl-1 or Bcl-XL using the BH3-like sequences derived from five wild-type pro-apoptotic BH3 peptides. Peptide-protein interaction energies calculated from these models for each set of BH3-like sequences resulted in negatively skewed extreme value distributions. The selected BH3-like sequences from the extreme negative tail regions have highly favorable interaction energies with Mcl-1 or Bcl-XL. They are enriched in acidic and basic residues when they bind to Mcl-1 and Bcl-XL, respectively. With the charged residues often away from the binding interface, the overall electric field generated by the charged residues results in strong long-range electrostatic interaction energies between the peptide and the protein giving rise to high specificity. Cell viability studies of representative BH3-like peptides further validated the predicted specificity. This study has revealed the importance of non-hot spot residues in BH3-mimetic peptides in providing specificity to a particular anti-apoptotic protein.
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Singh K, Briggs JM. Impact of lymphoma-linked Asn11Tyr point mutation on the interaction between Bcl-2 and a BH3 mimetic: Insights from molecular dynamics simulation. Chem Biol Drug Des 2020; 95:435-450. [PMID: 32030875 DOI: 10.1111/cbdd.13653] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/10/2019] [Accepted: 11/23/2019] [Indexed: 12/18/2022]
Abstract
Frequent mutations in the Bcl-2 anti-apoptotic protein are often implicated in diffuse large B-cell lymphoma (DLBCL), a disease profoundly resistant to drugs. Bcl-2-competitive inhibitors, "BH3 mimetics," activate apoptosis by interfering with the interactions between pro-apoptotic BH3 domains and the hydrophobic groove of Bcl-2. The aim of our research is to determine the potential of DLBCL-linked N11Y mutation to facilitate resistance against a "BH3 mimetic" using molecular dynamics simulation. Binding free energy calculations suggest a significant decrease in the binding affinity in the mutant model. In-depth analysis of the models using residue interaction network, dynamic cross-correlation, and free energy landscape approaches reveal that the mutation modifies the conformations of key residues, thereby altering the shape of the hydrophobic groove. This subsequently changes the ligand orientation and counteracts the phenomenon of LB region unwinding, a crucial event observed in the wild-type model. Lowest frequency motions captured by principal component analysis reflect the stretching of the groove for efficient ligand accommodation in the wild-type complex but not in the mutant model. This is the first in silico study that unravels the mechanism of drug resistance induced by a Bcl-2 mutation, which could be of great relevance while designing and tailoring therapeutics.
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Affiliation(s)
- Khushboo Singh
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - James M Briggs
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
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Kanakaveti V, Rathinasamy S, Rayala SK, Gromiha M. Forging New Scaffolds from Old: Combining Scaffold Hopping and Hierarchical Virtual Screening for Identifying Novel Bcl-2 Inhibitors. Curr Top Med Chem 2019; 19:1162-1172. [DOI: 10.2174/1568026619666190618142432] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 02/21/2019] [Accepted: 04/12/2019] [Indexed: 11/22/2022]
Abstract
Background:
Though virtual screening methods have proven to be potent in various instances, the
technique is practically incomplete to quench the need of drug discovery process. Thus, the quest for novel
designing approaches and chemotypes for improved efficacy of lead compounds has been intensified and logistic
approaches such as scaffold hopping and hierarchical virtual screening methods were evolved. Till now,
in all the previous attempts these two approaches were applied separately.
Objective:
In the current work, we made a novel attempt in terms of blending scaffold hopping and hierarchical
virtual screening. The prime objective is to assess the hybrid method for its efficacy in identifying active
lead molecules for emerging PPI target Bcl-2 (B-cell Lymphoma 2).
Method:
We designed novel scaffolds from the reported cores and screened a set of 8270 compounds using
both scaffold hopping and hierarchical virtual screening for Bcl-2 protein. Also, we enumerated the libraries
using clustering, PAINS filtering, physicochemical characterization and SAR matching.
Results:
We generated a focused library of compounds towards Bcl-2 interface, screened the 8270 compounds
and identified top hits for seven families upon fine filtering with PAINS algorithm, features, SAR mapping,
synthetic accessibility and similarity search. Our approach retrieved a set of 50 lead compounds.
Conclusions:
Finding rational approach meeting the needs of drug discovery process for PPI targets is the need
of the hour which can be fulfilled by an extended scaffold hopping approach resulting in focused PPI targeting
by providing novel leads with better potency.
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Affiliation(s)
- Vishnupriya Kanakaveti
- Protein Bioinformatics Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai – 600036, Tamil Nadu, India
| | - Sakthivel Rathinasamy
- Protein Bioinformatics Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai – 600036, Tamil Nadu, India
| | - Suresh K. Rayala
- Molecular Oncology Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai – 600036, Tamil Nadu, India
| | - Michael Gromiha
- Protein Bioinformatics Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai – 600036, Tamil Nadu, India
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Priya P, Maity A, Ghosh Dastidar S. The long unstructured region of Bcl-xl modulates its structural dynamics. Proteins 2017; 85:1567-1579. [PMID: 28486788 DOI: 10.1002/prot.25316] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 04/28/2017] [Accepted: 05/02/2017] [Indexed: 01/22/2023]
Abstract
Bcl-xl protein has a long unstructured loop attached to its structured region which joins two helices. The necessity to have this unstructured segment in Bcl-xl is not yet well understood. To what extent the unstructured segment can influence the dynamics of the structured region of protein, with potential to influence the function, has been investigated in this work. Molecular dynamics simulation and principal component analysis show how the loop affects the internal motions of the protein, particularly its ligand binding pocket. Generally an unstructured region in the structure would promote flexibility resulting entropic stability but in contrary, here it narrows down the conformational space of the structured region of protein that could be hypothesized to impact the functional precision. Effects of the loop propagate to the binding pocket through structural rearrangements of polar side chains. The immediate suspicion of possible impact of phosphorylation to modulate the function of the protein is proven to be a fact, as the phosphorylated S49 and S62 located on the large unstructured region are seen to perturb the electrostatic network of the structure; an observation that validates and clarifies the role of loop as a modulator through biophysical and biochemical mechanisms. Proteins 2017; 85:1567-1579. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Prerna Priya
- Bioinformatics Centre, Bose Institute, P-1/12 C.I.T Scheme VII M, Kolkata, 700054, India
| | - Atanu Maity
- Bioinformatics Centre, Bose Institute, P-1/12 C.I.T Scheme VII M, Kolkata, 700054, India
| | - Shubhra Ghosh Dastidar
- Bioinformatics Centre, Bose Institute, P-1/12 C.I.T Scheme VII M, Kolkata, 700054, India
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Modi V, Sankararamakrishnan R. Binding affinity of pro-apoptotic BH3 peptides for the anti-apoptotic Mcl-1 and A1 proteins: Molecular dynamics simulations of Mcl-1 and A1 in complex with six different BH3 peptides. J Mol Graph Model 2017; 73:115-128. [PMID: 28279820 DOI: 10.1016/j.jmgm.2016.12.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/29/2016] [Accepted: 12/08/2016] [Indexed: 02/07/2023]
Abstract
The anti-apoptotic members of Bcl-2 family of proteins bind to their pro-apoptotic counterparts to induce or prevent cell death.Based on the distinct binding profiles for specific pro-apoptotic BH3 peptides, the anti-apoptotic Bcl-2 proteins can be divided into at least two subclasses. The subclass that includes Bcl-XL binds strongly to Bad BH3 peptide while it has weak binding affinity for the second subclass of Bcl-2 proteins such as Mcl-1 and A1. Anti-apoptotic Bcl-2 proteins are considered to be attractive drug targets for anti-cancer drugs. BH3-mimetic inhibitors such as ABT-737 have been shown to be specific to Bcl-XL subclass while Mcl-1 and A1 show resistance to the same drug. An efficacious inhibitor should target all the anti-apoptotic Bcl-2 proteins. Hence, development of inhibitors selective to Mcl-1 and A1 is of prime importance for targeted cancer therapeutics. The first step to achieve this goal is to understand the molecular basis of high binding affinities of specific pro-apoptotic BH3 peptides for Mcl-1 and A1. To understand the interactions between the BH3 peptides and Mcl-1/A1, we performed multi-nanosecond molecular dynamics (MD) simulations of six complex structures of Mcl-1 and A1. With the exception of Bad, all complex structures were experimentally determined. Bad complex structures were modeled. Our simulation studies identified specific pattern of polar interactions between Mcl-1/A1 and high-affinity binding BH3 peptides. The lack of such polar interactions in Bad peptide complex is attributed to specific basic residues present before and after the highly conserved Leu residue. The close approach of basic residues in Bad and Mcl-1/A1 is hypothesized to be the cause of weak binding affinity. To test this hypothesis, we generated in silico mutants of these basic residues in Bad peptide and Mcl-1/A1 proteins. MD simulations of the mutant systems established the pattern of stable polar interactions observed in high-affinity binding BH3 peptides. We have thus identified specific residue positions in Bad and Mcl-1/A1 responsible for the weak binding affinity. Results from these simulation studies will aid in the development of inhibitors specific to Mcl-1 and A1 proteins.
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Affiliation(s)
- Vivek Modi
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, 208016, India
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Lama D, Brown CJ, Lane DP, Verma CS. Gating by Tryptophan 73 Exposes a Cryptic Pocket at the Protein-Binding Interface of the Oncogenic eIF4E Protein. Biochemistry 2015; 54:6535-44. [DOI: 10.1021/acs.biochem.5b00812] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Dilraj Lama
- Bioinformatics
Institute, A*STAR (Agency for Science, Technology and Research), 30 Biopolis
Street, #07-01 Matrix, Singapore 138671
| | - Christopher J. Brown
- p53
Laboratory, A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove, #06-04/05, Neuros/Immunos, Singapore 138648
| | - David P. Lane
- p53
Laboratory, A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove, #06-04/05, Neuros/Immunos, Singapore 138648
| | - Chandra S. Verma
- Bioinformatics
Institute, A*STAR (Agency for Science, Technology and Research), 30 Biopolis
Street, #07-01 Matrix, Singapore 138671
- Department
of Biological Sciences, National University of Singapore, 14 Science
Drive 4, Singapore 117543
- School
of Biological Sciences, Nanyang Technological University, 50 Nanyang
Drive, Singapore 637551
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8
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Chu M, Ding R, Chu ZY, Zhang MB, Liu XY, Xie SH, Zhai YJ, Wang YD. Role of berberine in anti-bacterial as a high-affinity LPS antagonist binding to TLR4/MD-2 receptor. BMC COMPLEMENTARY AND ALTERNATIVE MEDICINE 2014; 14:89. [PMID: 24602493 PMCID: PMC3946165 DOI: 10.1186/1472-6882-14-89] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2013] [Accepted: 02/18/2014] [Indexed: 12/14/2022]
Abstract
BACKGROUND Berberine is an isoquinoline alkaloid mainly extracted from Rhizoma Coptidis and has been shown to possess a potent inhibitory activity against bacterial. However, the role of berberine in anti-bacterial action has not been extensively studied. METHODS The animal model was established to investigate the effects of berberine on bacterial and LPS infection. Docking analysis, Molecular dynamics simulations and Real-time RT-PCR analysis was adopted to investigate the molecular mechanism. RESULTS Treatment with 40 mg/kg berberine significantly increased the survival rate of mice challenged with Salmonella typhimurium (LT2), but berberine show no effects in bacteriostasis. Further study indicated that treatment with 0.20 g/kg berberine markedly increased the survival rate of mice challenged with 2 EU/ml bacterial endotoxin (LPS) and postpone the death time of the dead mice. Moreover, pretreatment with 0.05 g/kg berberine significantly lower the increasing temperature of rabbits challenged with LPS. The studies of molecular mechanism demonstrated that Berberine was able to bind to the TLR4/MD-2 receptor, and presented higher affinity in comparison with LPS. Furthermore, berberine could significantly suppressed the increasing expression of NF-κB, IL-6, TNFα, and IFNβ in the RAW264.7 challenged with LPS. CONCLUSION Berberine can act as a LPS antagonist and block the LPS/TLR4 signaling from the sourse, resulting in the anti-bacterial action.
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Han E, Lee H. Effect of the structural difference between Bax-α5 and Bcl-xL-α5 on their interactions with lipid bilayers. Phys Chem Chem Phys 2014; 16:981-8. [DOI: 10.1039/c3cp53486c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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10
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Modi V, Sankararamakrishnan R. Antiapoptotic Bcl-2 homolog CED-9 in Caenorhabditis elegans
: Dynamics of BH3 and CED-4 binding regions and comparison with mammalian antiapoptotic Bcl-2 proteins. Proteins 2013; 82:1035-47. [DOI: 10.1002/prot.24476] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Revised: 10/16/2013] [Accepted: 11/04/2013] [Indexed: 12/29/2022]
Affiliation(s)
- Vivek Modi
- Department of Biological Sciences & Bioengineering; Indian Institute of Technology Kanpur; Kanpur 208016 India
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