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Rao RN, Das S, Jacob K, Alam MM, Balamurali MM, Chanda K. Synthetic access to diverse thiazetidines via a one-pot microwave assisted telescopic approach and their interaction with biomolecules. Org Biomol Chem 2024; 22:3249-3261. [PMID: 38568016 DOI: 10.1039/d4ob00075g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
A one-pot microwave assisted telescopic approach is reported for the chemo-selective synthesis of substituted 1,3-thiazetidines using readily available 2-aminopyridines/pyrazines/pyrimidine, substituted isothiocyanates and 1,2-dihalomethanes. The procedure involves thiourea formation from 2-aminopyridines/pyrazines/pyrimidine with the substituted isothiocyanates followed by a base catalysed nucleophilic attack of the CS bond on the 1,2-dihalomethane. Subsequently, a cyclization reaction occurs to yield substituted 1,3-thiazetidines. These four membered strained ring systems are reported to possess broad substrate scope with high functional group tolerance. The above synthetic sequence for the formation of four membered heterocycles is proven to be a modular and straightforward approach. Further the mechanistic pathway for the formation of 1,3-thiazetidines was supported by computational evaluations and X-ray crystallography analyses. The relevance of these thiazetidines in biological applications is evaluated by studying their ability to bind bio-macromolecules like proteins and nucleic acids.
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Affiliation(s)
- Ramdas Nishanth Rao
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore 632014, India.
| | - Soumyadip Das
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore 632014, India.
| | - Kezia Jacob
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore 632014, India.
| | - Mohammed Mujahid Alam
- Department of Chemistry, College of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - M M Balamurali
- Chemistry Division, School of Advanced Sciences, Vellore Institute of Technology, Chennai, Tamil Nadu, 600027, India.
| | - Kaushik Chanda
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore 632014, India.
- Department of Chemistry, Rabindranath Tagore University, Hojai 782435, Assam, India
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Venkatesan S, Chanda K, Balamurali MM. An in silico approach to investigate the theranostic potential of coumarin-derived self-immolative luminescent probes. Chem Biodivers 2024; 21:e202301400. [PMID: 38109279 DOI: 10.1002/cbdv.202301400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/07/2023] [Accepted: 12/17/2023] [Indexed: 12/20/2023]
Abstract
Till date the challenge exists in the treatments of cancer for various reasons. Most importantly, the available diagnostics are expensive with research gap for enhancing the cancer detection sensitivity. Herein, a series of coumarin-derived fluorescent theranostic probes are reported that can serve as potent anticancer agents as well as in the detection of cancer cells. The potential of these probes to efficiently block one of the well-known cancer drug targets NADPH quinone oxidoreductase-1 (NQO1) is evaluated through various pharmacokinetic methods including absorption, distribution, metabolism and excretion (ADME) properties evaluation, PASS (prediction of activity spectra for substance) algorithm along with molecular docking and dynamic simulations. Further the luminescent properties of these molecules were evaluated by investigating their electronic properties in the ground and excited states with the help of density functional theory methods. Results indicate that the proposed molecules can potentially block the NADPH (reduced form of nicotinamide adenine dinucleotide) binding site of NQO1, thereby inhibiting the activity of the enzyme to ultimately disrupt the metabolism of cancer cells.
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Affiliation(s)
- Swathi Venkatesan
- Chemistry Division, School of Advanced Sciences, Vellore Institute of Technology, Chennai, Tamil Nadu, India, 600027
| | - Kaushik Chanda
- Department of Chemistry, Rabindranath Tagore University, Hojai, Assam, India, 782435
| | - M M Balamurali
- Chemistry Division, School of Advanced Sciences, Vellore Institute of Technology, Chennai, Tamil Nadu, India, 600027
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3
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Abstract
The Click reaction that involves Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) serves as the most potent and highly dependable tool for the development of many complex architectures. It has paved the way for the synthesis of numerous drug molecules with enhanced synthetic flexibility, reliability, specificity and modularity. It is all about bringing two different molecular entities together to achieve the required molecular properties. The utilization of Click chemistry has been well demonstrated in organic synthesis, particularly in reactions that involve biocompatible precursors. In pharmaceutical research, Click chemistry is extensively utilized for drug delivery applications. The exhibited bio-compatibility and dormancy towards other biological components under cellular environments makes Click chemistry an identified boon in bio-medical research. In this review, various click-derived transition metal complexes are discussed in terms of their applications and uniqueness. The scope of this chemistry towards other streams of applied sciences is also discussed.
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Affiliation(s)
- Md Gulzar Ahmad
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore 632014, Tamilnadu, India.
| | - M M Balamurali
- Chemistry Division, School of Advanced Sciences, Vellore Institute of Technology, Chennai campus, Chennai 600127, Tamilnadu, India.
| | - Kaushik Chanda
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore 632014, Tamilnadu, India.
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Jena S, Choudhury B, Ahmad MG, Balamurali MM, Chanda K. Photophysical evaluation on the electronic properties of synthesized biologically significant pyrido fused imidazo[4,5-c]quinolines. Spectrochim Acta A Mol Biomol Spectrosc 2023; 287:122081. [PMID: 36379086 DOI: 10.1016/j.saa.2022.122081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/19/2022] [Accepted: 11/02/2022] [Indexed: 06/16/2023]
Abstract
A single pot microwave assisted method was employed to synthesize a series of novel pyrido fused imidazo[4,5-c]quinolines. The electronic properties of these derivatives were investigated by following their photophysical behaviour under isolated and solvated conditions via computational and experimental approaches. The solvatochromic effect of these derivatives was investigated in the ground and excited singlet states by following the absorption and fluorescence emission and excitation spectra. Further the effect of general and specific solvent effects were also investigated by plotting Stokes shift against Lippert-Mataga, ET(30) and Kamlet-Taft polarity parameters respectively. The deviation from linearity in ET(30) plot indicates that formation of different species in polar protic solvents. The biological applications of these derivatives as potential drug candidates were evaluated by in silico computational methods followed by pharmacokinetic properties predictions. The ability of these derivatives to inhibit human casein kinase 2 (CK2) was evaluated. The structure activity relationships were correlated by evaluating the electronic properties through experimental photophysical investigations including solvatochromic effect and computational electronic structure calculations. Of the various derivatives, p-nitro phenyl substituted pyrido fused imidazo[4,5-c]quinoline exhibited good inhibitory activity against CK2 enzyme and hence could serve as a promising drug candidate.
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Affiliation(s)
- Sushovan Jena
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore 632 014, Tamil Nadu, India
| | - Badruzzaman Choudhury
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore 632 014, Tamil Nadu, India
| | - Md Gulzar Ahmad
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore 632 014, Tamil Nadu, India
| | - M M Balamurali
- Division of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Chennai Campus, Vandalur-Kelambakkam Road, Chennai 600 127, Tamil Nadu, India.
| | - Kaushik Chanda
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore 632 014, Tamil Nadu, India.
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5
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Prathima TS, Ahmad MG, Karuppasamy R, Chanda K, Balamurali MM. Investigation on Phyto‐active Constituent of
Clerodendrum paniculatum
as Therapeutic Agent against Viral Diseases. ChemistrySelect 2023. [DOI: 10.1002/slct.202203932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- T. S. Prathima
- Division of Chemistry School of Advanced Sciences Vellore Institute of Technology Chennai Tamil Nadu India 600027
| | - Md. Gulzar Ahmad
- Department of Chemistry School of Advanced Sciences Vellore Institute of Technology Vellore Tamil Nadu India 632014
| | - Ramanathan Karuppasamy
- Department of Biotechnology School of BioSciences and Technology Vellore Institute of Technology Vellore Tamil Nadu India 632014
| | - Kaushik Chanda
- Department of Chemistry School of Advanced Sciences Vellore Institute of Technology Vellore Tamil Nadu India 632014
| | - M. M. Balamurali
- Division of Chemistry School of Advanced Sciences Vellore Institute of Technology Chennai Tamil Nadu India 600027
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6
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Rajasekhar S, Das S, Balamurali MM, Chanda K. Therapeutic Inhibitory Activities of
N
‐Hydroxy Derived Cytidines: A Patent Overview. ChemistrySelect 2021. [DOI: 10.1002/slct.202102856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Sreerama Rajasekhar
- Department of Chemistry School of Advanced Sciences Vellore Institute of Technology Vellore 632014 India
| | - Soumyadip Das
- Department of Chemistry School of Advanced Sciences Vellore Institute of Technology Vellore 632014 India
| | - M. M. Balamurali
- Division of Chemistry School of Advanced Sciences Vellore Institute of Technology, Chennai campus Vandalur-Kelambakkam Road Chennai 600 127 Tamil Nadu India
| | - Kaushik Chanda
- Department of Chemistry School of Advanced Sciences Vellore Institute of Technology Vellore 632014 India
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7
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Selvendran S, Das S, Waidha K, Venkatesan S, Balamurali MM, Basu B, Rajendran S. Pyrrole‐Fused Benzoxazinones/Quinoxalinones: Molecular Dynamic Simulation, Antiproliferative and Antibacterial Activities. ChemistrySelect 2021. [DOI: 10.1002/slct.202103015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Suresh Selvendran
- Chemistry Division School of Advanced Sciences Vellore Institute of Technology Chennai Campus Chennai 600127 Tamilnadu India
| | - Souvik Das
- Department of Neuroendocrinology and Experimental Hematology Chittaranjan National Cancer Institute Kolkata 700 026 West Bengal India
| | - Kamran Waidha
- DRDO-Defence Institute of High Altitude Research (DIHAR), Leh Ladakh, UT 194101 India
| | - Swathi Venkatesan
- Chemistry Division School of Advanced Sciences Vellore Institute of Technology Chennai Campus Chennai 600127 Tamilnadu India
| | - M. M. Balamurali
- Chemistry Division School of Advanced Sciences Vellore Institute of Technology Chennai Campus Chennai 600127 Tamilnadu India
| | - Biswarup Basu
- Department of Neuroendocrinology and Experimental Hematology Chittaranjan National Cancer Institute Kolkata 700 026 West Bengal India
| | - Saravanakumar Rajendran
- Chemistry Division School of Advanced Sciences Vellore Institute of Technology Chennai Campus Chennai 600127 Tamilnadu India
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8
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Subramani M, Ramamoorthy G, Hemaiswarya S, Waidha K, Brindha J, Balamurali MM, Doble M, Rajendran S. Hydroxy Piperlongumines: Synthesis, Antioxidant, Cytotoxic Effect on Human Cancer Cell Lines, Inhibitory Action and ADMET Studies. ChemistrySelect 2020. [DOI: 10.1002/slct.202002453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Muthuraman Subramani
- Chemistry division School of Advanced Sciences Vellore Institute of Technology Chennai 600127 Tamilnadu India
| | - Gayathri Ramamoorthy
- Department of Biotechnology Indian Institute of Technology Madras Tamilnadu 600036 India
| | - Shanmugam Hemaiswarya
- Department of Biotechnology Indian Institute of Technology Madras Tamilnadu 600036 India
| | - Kamran Waidha
- Amity Institute of Biotechnology Amity University Uttar Pradesh, Sector-125 Noida 201303 India
| | - J. Brindha
- Chemistry division School of Advanced Sciences Vellore Institute of Technology Chennai 600127 Tamilnadu India
| | - M. M. Balamurali
- Chemistry division School of Advanced Sciences Vellore Institute of Technology Chennai 600127 Tamilnadu India
| | - Mukesh Doble
- Department of Biotechnology Indian Institute of Technology Madras Tamilnadu 600036 India
| | - Saravanakumar Rajendran
- Chemistry division School of Advanced Sciences Vellore Institute of Technology Chennai 600127 Tamilnadu India
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9
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Kiran T, Pathak M, Chanda K, Balamurali MM. DNA and Protein Interaction Studies of Heteroleptic Copper (II) Derivatives of Benzothiazole‐Based Schiff Base and N,N‐Donor Ligands. ChemistrySelect 2020. [DOI: 10.1002/slct.202001246] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Tummalapalli Kiran
- Department of ChemistryScience and HumanitiesJ. B. Institute of Engineering and Technology Moinabad Hyderabad 500075 India
| | - Madhvesh Pathak
- Department of ChemistrySchool of Advanced SciencesVellore Institute of Technology Vellore 632014 Tamilnadu India
| | - Kaushik Chanda
- Department of ChemistrySchool of Advanced SciencesVellore Institute of Technology Vellore 632014 Tamilnadu India
| | - M. M. Balamurali
- Chemistry DivisionSchool of Advanced SciencesVellore Institute of Technology Chennai Campus Chennai 600127 Tamilnadu India
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10
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Muthuraman S, Sinha S, Vasavi CS, Waidha KM, Basu B, Munussami P, Balamurali MM, Doble M, Saravana Kumar R. Design, synthesis and identification of novel coumaperine derivatives for inhibition of human 5-LOX: Antioxidant, pseudoperoxidase and docking studies. Bioorg Med Chem 2019; 27:604-619. [PMID: 30638966 DOI: 10.1016/j.bmc.2018.12.043] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 12/14/2018] [Accepted: 12/31/2018] [Indexed: 01/09/2023]
Abstract
5-Lipoxygenase (5-LOX) is a key enzyme involved in the biosynthesis of pro-inflammatory leukotrienes, leading to asthma. Developing potent 5-LOX inhibitors especially, natural product based ones, are highly attractive. Coumaperine, a natural product found in white pepper and its derivatives were herein developed as 5-LOX inhibitors. We have synthesized twenty four derivatives, characterized and evaluated their 5-LOX inhibition potential. Coumaperine derivatives substituted with multiple hydroxy and multiple methoxy groups exhibited best 5-LOX inhibition. CP-209, a catechol type dihydroxyl derivative and CP-262-F2, a vicinal trihydroxyl derivative exhibited, 82.7% and 82.5% inhibition of 5-LOX respectively at 20 µM. Their IC50 values are 2.1 ± 0.2 µM and 2.3 ± 0.2 µM respectively, and are comparable to zileuton, IC50 = 1.4 ± 0.2 µM. CP-155, a methylenedioxy derivative (a natural product) and CP-194, a 2,4,6-trimethoxy derivative showed 76.0% and 77.1% inhibition of 5-LOX respectively at 20 µM. Antioxidant study revealed that CP-209 and 262-F2 (at 20 µM) scavenged DPPH radical by 76.8% and 71.3% respectively. On the other hand, CP-155 and 194 showed very poor DPPH radical scavenging activity. Pseudo peroxidase assay confirmed that the mode of action of CP-209 and 262-F2 were by redox process, similar to zileuton, affecting the oxidation state of the metal ion in the enzyme. On the contrary, CP-155 and 194 probably act through some other mechanism which does not involve the disruption of the oxidation state of the metal in the enzyme. Molecular docking of CP-155 and 194 to the active site of 5-LOX and binding energy calculation suggested that they are non-competitive inhibitors. The In-Silico ADME/TOX analysis shows the active compounds (CP-155, 194, 209 and 262-F2) are with good drug likeliness and reduced toxicity compared to existing drug. These studies indicate that there is a great potential for coumaperine derivatives to be developed as anti-inflammatory drug.
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Affiliation(s)
- Subramani Muthuraman
- Chemistry Division, School of Advanced Sciences, Vellore Institute of Technology, Chennai 600127, Tamilnadu, India
| | - Shweta Sinha
- Department of Chemistry, Vellore Institute of Technology, Vellore, Tamilnadu 632014, India; Department of Biotechnology, Indian Institute of Technology, Madras, Tamilnadu 600036, India.
| | - C S Vasavi
- Bioinformatics Division, School of Biosciences and Technology, VIT University, Vellore, Tamilnadu 632 014, India
| | - Kamran Manzoor Waidha
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, sector-125, Noida 201303, India
| | - Biswarup Basu
- Department of Neuroendocrinology, Chittaranjan National Cancer Institute, 37 S P Mukherjee Road, Kolkata 700026,India
| | - Punnagai Munussami
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Gachibowli, Hyderabad 500 032, India
| | - M M Balamurali
- Chemistry Division, School of Advanced Sciences, Vellore Institute of Technology, Chennai 600127, Tamilnadu, India
| | - Mukesh Doble
- Department of Biotechnology, Indian Institute of Technology, Madras, Tamilnadu 600036, India
| | - Rajendran Saravana Kumar
- Chemistry Division, School of Advanced Sciences, Vellore Institute of Technology, Chennai 600127, Tamilnadu, India.
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12
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Kumar S, Balamurali MM, Sankaran K. Bacterial lipid modification of proteins requires appropriate secretory signals even for expression - implications for biogenesis and protein engineering. Mol Membr Biol 2014; 31:183-94. [PMID: 25156679 DOI: 10.3109/09687688.2014.943819] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Sec- and Tat-mediated bacterial lipid modification of proteins are important posttranslational processes owing to their vital roles in cellular functions, membrane targeting and biotechnological applications like ELISA, biosensor, adjuvant-free vaccines, liposomal drug delivery etc. However a better understanding of the tight coupling of secretory and lipid modification machineries and the processes associated will help unravel this essential biological event and utilize it for engineering applications. Further, there is a need for a systematic and convincing investigation into membrane targeting, solubilization and ease-of-purification of engineered lipoproteins to facilitate scientists in readily applying this new protein engineering tool. Therefore, in this study, we have investigated systematically recombinant expression, translocation, solubilization and purification of three White Spot Syndrome Viral (WSSV) proteins, ICP11, VP28 and VP281. Our study shows that the lipid modification and secretion processes are tightly coupled to the extent that mismatch between folding kinetics and signal sequence of target proteins could lead to transcriptional-translational uncoupling or aborted translation. The proteins expressed as lipoproteins through Tat-pathway were targeted to the inner membrane achieving considerable enrichment. These His-tagged proteins were then purified to apparent homogeneity in detergent-free form using single-step Immobilized Metal Affinity Chromatography. This study has interesting findings in lipoprotein biogenesis enhancing the scope of this unique post-translational protein engineering tool for obtaining pure detergent-free, membrane or hydrophobic surface-associating diagnostic targets and vaccine candidates for WSSV.
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13
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Saha P, Barua B, Bhattacharyya S, Balamurali MM, Schief WR, Baker D, Varadarajan R. Design and characterization of stabilized derivatives of human CD4D12 and CD4D1. Biochemistry 2011; 50:7891-900. [PMID: 21827143 DOI: 10.1021/bi200870r] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
CD4 is present on the surface of T-lymphocytes and is the primary cellular receptor for HIV-1. CD4 consists of a cytoplasmic tail, one transmembrane region, and four extracellular domains, D1-D4. A construct consisting of the first two domains of CD4 (CD4D12) is folded and binds gp120 with similar affinity as soluble 4-domain CD4 (sCD4). However, the first domain alone (CD4D1) was previously shown to be largely unfolded and had 3-fold weaker affinity for gp120 when compared to sCD4 [Sharma, D.; et al. (2005) Biochemistry 44, 16192-16202]. We now report the design and characterization of three single-site mutants of CD4D12 (G6A, L51I, and V86L) and one multisite mutant of CD4D1 (G6A/L51I/L5K/F98T). G6A, L51I, and V86L are cavity-filling mutations while L5K and F98T are surface mutations which were introduced to minimize the aggregation of CD4D1 upon removal of the second domain. Two mutations, G6A and V86L in CD4D12 increased the stability and yield of the protein relative to the wild-type protein. The mutant CD4D1 (CD4D1a) with the 4 mutations was folded and more stable compared to the original CD4D1, but both bound gp120 with comparable affinity. In in vitro neutralization assays, both CD4D1a and G6A-CD4D12 were able to neutralize diverse HIV-1 viruses with similar IC(50)s as 4-domain CD4. These stabilized derivatives of human CD4 can be useful starting points for the design of other more complex viral entry inhibitors.
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Affiliation(s)
- Piyali Saha
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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14
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Aggarwal V, Kulothungan SR, Balamurali MM, Saranya SR, Varadarajan R, Ainavarapu SRK. Ligand-modulated parallel mechanical unfolding pathways of maltose-binding proteins. J Biol Chem 2011; 286:28056-65. [PMID: 21659518 DOI: 10.1074/jbc.m111.249045] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Protein folding and unfolding are complex phenomena, and it is accepted that multidomain proteins generally follow multiple pathways. Maltose-binding protein (MBP) is a large (a two-domain, 370-amino acid residue) bacterial periplasmic protein involved in maltose uptake. Despite the large size, it has been shown to exhibit an apparent two-state equilibrium unfolding in bulk experiments. Single-molecule studies can uncover rare events that are masked by averaging in bulk studies. Here, we use single-molecule force spectroscopy to study the mechanical unfolding pathways of MBP and its precursor protein (preMBP) in the presence and absence of ligands. Our results show that MBP exhibits kinetic partitioning on mechanical stretching and unfolds via two parallel pathways: one of them involves a mechanically stable intermediate (path I) whereas the other is devoid of it (path II). The apoMBP unfolds via path I in 62% of the mechanical unfolding events, and the remaining 38% follow path II. In the case of maltose-bound MBP, the protein unfolds via the intermediate in 79% of the cases, the remaining 21% via path II. Similarly, on binding to maltotriose, a ligand whose binding strength with the polyprotein is similar to that of maltose, the occurrence of the intermediate is comparable (82% via path I) with that of maltose. The precursor protein preMBP also shows a similar behavior upon mechanical unfolding. The percentages of molecules unfolding via path I are 53% in the apo form and 68% and 72% upon binding to maltose and maltotriose, respectively, for preMBP. These observations demonstrate that ligand binding can modulate the mechanical unfolding pathways of proteins by a kinetic partitioning mechanism. This could be a general mechanism in the unfolding of other large two-domain ligand-binding proteins of the bacterial periplasmic space.
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Affiliation(s)
- Vasudha Aggarwal
- Department of Biological Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai 400 005, India
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15
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Pain J, Balamurali MM, Dancis A, Pain D. Mitochondrial NADH kinase, Pos5p, is required for efficient iron-sulfur cluster biogenesis in Saccharomyces cerevisiae. J Biol Chem 2010; 285:39409-24. [PMID: 20889970 PMCID: PMC2998133 DOI: 10.1074/jbc.m110.178947] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 09/30/2010] [Indexed: 11/06/2022] Open
Abstract
In Saccharomyces cerevisiae, the mitochondrial inner membrane readily allows transport of cytosolic NAD(+), but not NADPH, to the matrix. Pos5p is the only known NADH kinase in the mitochondrial matrix. The enzyme phosphorylates NADH to NADPH and is the major source of NADPH in the matrix. The importance of mitochondrial NADPH for cellular physiology is underscored by the phenotypes of the Δpos5 mutant, characterized by oxidative stress sensitivity and iron-sulfur (Fe-S) cluster deficiency. Fe-S clusters are essential cofactors of proteins such as aconitase [4Fe-4S] and ferredoxin [2Fe-2S] in mitochondria. Intact mitochondria isolated from wild-type yeast can synthesize these clusters and insert them into the corresponding apoproteins. Here, we show that this process of Fe-S cluster biogenesis in wild-type mitochondria is greatly stimulated and kinetically favored by the addition of NAD(+) or NADH in a dose-dependent manner, probably via transport into mitochondria and subsequent conversion into NADPH. Unlike wild-type mitochondria, Δpos5 mitochondria cannot efficiently synthesize Fe-S clusters on endogenous aconitase or imported ferredoxin, although cluster biogenesis in isolated Δpos5 mitochondria is restored to a significant extent by a small amount of imported Pos5p. Interestingly, Fe-S cluster biogenesis in wild-type mitochondria is further enhanced by overexpression of Pos5p. The effects of Pos5p on Fe-S cluster generation in mitochondria indicate that one or more steps in the biosynthetic process require NADPH. The role of mitochondrial NADPH in Fe-S cluster biogenesis appears to be distinct from its function in anti-oxidant defense.
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Affiliation(s)
- Jayashree Pain
- From the Department of Pharmacology and Physiology, University of Medicine and Dentistry of New Jersey, New Jersey Medical School, Newark, New Jersey 07101 and
| | - M. M. Balamurali
- From the Department of Pharmacology and Physiology, University of Medicine and Dentistry of New Jersey, New Jersey Medical School, Newark, New Jersey 07101 and
| | - Andrew Dancis
- the Department of Medicine, Division of Hematology-Oncology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Debkumar Pain
- From the Department of Pharmacology and Physiology, University of Medicine and Dentistry of New Jersey, New Jersey Medical School, Newark, New Jersey 07101 and
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Lv S, Dudek DM, Cao Y, Balamurali MM, Gosline J, Li H. Designed biomaterials to mimic the mechanical properties of muscles. Nature 2010; 465:69-73. [DOI: 10.1038/nature09024] [Citation(s) in RCA: 409] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Accepted: 03/09/2010] [Indexed: 11/09/2022]
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Balamurali MM, Sharma D, Chang A, Khor D, Chu R, Li H. Recombination of protein fragments: a promising approach toward engineering proteins with novel nanomechanical properties. Protein Sci 2008; 17:1815-26. [PMID: 18628239 DOI: 10.1110/ps.036376.108] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Combining single molecule atomic force microscopy (AFM) and protein engineering techniques, here we demonstrate that we can use recombination-based techniques to engineer novel elastomeric proteins by recombining protein fragments from structurally homologous parent proteins. Using I27 and I32 domains from the muscle protein titin as parent template proteins, we systematically shuffled the secondary structural elements of the two parent proteins and engineered 13 hybrid daughter proteins. Although I27 and I32 are highly homologous, and homology modeling predicted that the hybrid daughter proteins fold into structures that are similar to that of parent protein, we found that only eight of the 13 daughter proteins showed beta-sheet dominated structures that are similar to parent proteins, and the other five recombined proteins showed signatures of the formation of significant alpha-helical or random coil-like structure. Single molecule AFM revealed that six recombined daughter proteins are mechanically stable and exhibit mechanical properties that are different from the parent proteins. In contrast, another four of the hybrid proteins were found to be mechanically labile and unfold at forces that are lower than the approximately 20 pN, as we could not detect any unfolding force peaks. The last three hybrid proteins showed interesting duality in their mechanical unfolding behaviors. These results demonstrate the great potential of using recombination-based approaches to engineer novel elastomeric protein domains of diverse mechanical properties. Moreover, our results also revealed the challenges and complexity of developing a recombination-based approach into a laboratory-based directed evolution approach to engineer novel elastomeric proteins.
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Affiliation(s)
- M M Balamurali
- Department of Chemistry, The University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
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Abstract
Protein-ligand interactions, including protein-protein interactions, are ubiquitously essential in biological processes and also have important applications in biotechnology. A wide range of methodologies have been developed for quantitative analysis of protein-ligand interactions. However, most of them do not report direct functional/structural consequence of ligand binding. Instead they only detect the change of physical properties, such as fluorescence and refractive index, because of the colocalization of protein and ligand, and are susceptible to false positives. Thus, important information about the functional state of protein-ligand complexes cannot be obtained directly. Here we report a functional single-molecule binding assay that uses force spectroscopy to directly probe the functional consequence of ligand binding and report the functional state of protein-ligand complexes. As a proof of principle, we used protein G and the Fc fragment of IgG as a model system in this study. Binding of Fc to protein G does not induce major structural changes in protein G but results in significant enhancement of its mechanical stability. Using mechanical stability of protein G as an intrinsic functional reporter, we directly distinguished and quantified Fc-bound and Fc-free forms of protein G on a single-molecule basis and accurately determined their dissociation constant. This single-molecule functional binding assay is label-free, nearly background-free, and can detect functional heterogeneity, if any, among protein-ligand interactions. This methodology opens up avenues for studying protein-ligand interactions in a functional context, and we anticipate that it will find broad application in diverse protein-ligand systems.
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Affiliation(s)
- Yi Cao
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada V6T 1Z1
| | - M. M. Balamurali
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada V6T 1Z1
| | - Deepak Sharma
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada V6T 1Z1
| | - Hongbin Li
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada V6T 1Z1
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Sharma D, Balamurali MM, Chakraborty K, Kumaran S, Jeganathan S, Rashid U, Ingallinella P, Varadarajan R. Protein minimization of the gp120 binding region of human CD4. Biochemistry 2006; 44:16192-202. [PMID: 16331979 DOI: 10.1021/bi051120s] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
CD4 is an important component of the immune system and is also the cellular receptor for HIV-1. CD4 consists of a cytoplasmic tail, one transmembrane region, and four extracellular domains, D1-D4. Constructs consisting of all four extracellular domains of human CD4 as well as the first two domains (CD4D12) have previously been expressed and characterized. All of the gp120-binding residues are located within the first N-terminal domain (D1) of CD4. To date, it has not been possible to obtain domain D1 alone in a soluble and active form. Most residues in CD4 that interact with gp120 lie within the region 21-64 of domain D1 of CD4. On the basis of these observations and analysis of the crystal structure of CD4D12, a mutational strategy was designed to express CD4D1 and region 21-64 of CD4 (CD4PEP1) in Escherichia coli. K(D) values for the binding of CD4 analogues described above to gp120 were measured using a Biacore-based solution-phase competition binding assay. Measured K(D) values were 15 nM, 40 nM, and 26 microM for CD4D12, CD4D1, and CD4PEP1, respectively. All of the proteins interact with gp120 and are able to expose the 17b-binding epitope of gp120. Structural content was determined using CD and proteolysis. Both CD4D1 and CD4PEP1 were partially structured and showed an enhanced structure in the presence of the osmolyte sarcosine. The aggregation behavior of all of the proteins was characterized. While CD4D1 and CD4PEP1 did not aggregate, CD4D12 formed amyloid fibrils at neutral pH within a week at 278 K. These CD4 derivatives should be useful tools in HIV vaccine design and entry inhibition studies.
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Affiliation(s)
- Deepak Sharma
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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