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A Method Of Identifying Binding Sites Of A Molecule Of Interest On A Receptor Protein

Abstract: The present disclosure provides a rapid, scalable, and high-throughput method of identifying the precise regions in a receptor protein which are involved in binding of a molecule of interest. The method of the instant disclosure is useful where the crystal structure of a protein of interest is not available. Also provided are surface display libraries, and methods of making the same.

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Notices, Deadlines & Correspondence

Patent Information

Application #
Filing Date
08 December 2016
Publication Number
24/2018
Publication Type
INA
Invention Field
PHYSICS
Status
Email
Parent Application
Patent Number
Legal Status
Grant Date
2023-04-19
Renewal Date

Applicants

INDIAN INSTITUTE OF SCIENCE
Indian Institute of Science, C V Raman Avenue, Bangalore, Karnataka 560012, India.

Inventors

1. VARADARAJAN, Raghavan
Molecular Biophysics Unit, Indian Institute of Science, CV Raman Avenue, Bangalore 560012, India
2. NAJAR, Tariq Ahmad
Molecular Biophysics Unit, Indian Institute of Science, CV Raman Avenue, Bangalore 560012, India

Specification

1. A method of identifying binding sites of a molecule of interest on a receptor
protein, said method comprising:
a. obtaining a display population, wherein said population comprises cells, phage or
virus (hereafter collectively referred to for convenience as ‘cells’), each member
expressing on its surface a single mutant variant of the receptor protein, wherein
said mutant variant has a single amino acid residue mutated to cysteine;
b. contacting a cysteine specific probe with said population, wherein said cysteine
specific probe binds to cysteine residue on mutant variant;
c. contacting said molecule of interest with the display population; and
d. detecting binding of molecule of interest to mutant variant of receptor protein,
wherein lack of binding of molecule of interest to the mutant variant is indicative that the corresponding amino acid residue in the non-mutated receptor protein at the same position is involved in molecule of interest binding to receptor protein.
2. A method of identifying binding sites of a molecule of interest on a receptor
protein, said method comprising:
a. obtaining a display population, wherein said population comprises cells, each
member expressing on its surface a single mutant variant of the receptor protein,
wherein said mutant variant has a single amino acid residue mutated to cysteine
or alanine or serine or any other amino acid;
b. contacting a cysteine specific probe with said population, wherein said cysteine
specific probe binds to cysteine residue on mutant variant;
c. contacting said molecule of interest with the display population; and
d. detecting binding of molecule of interest to mutant variant of receptor protein,
wherein lack of binding of molecule of interest to the mutant variant is indicative that the corresponding amino acid residue in the non-mutated receptor protein at the same position is involved in molecule of interest binding to receptor protein.

3. The method as claimed in claim 1 or 2, wherein said receptor protein has no cysteine residues, and said mutant variant has a single mutation, wherein said mutation is a substituted cysteine.
4. The method as claimed in claim 1 or 2, wherein said receptor protein has “n” number of cysteine residues involved in binding of molecule of interest, and in said mutant variant, the “n” number of cysteine residues of the receptor protein are substituted with alanine or serine or any other amino acid, and further, an additional single substitution to cysteine is made at an amino acid position which is not any of the “n” number of cysteine residues in the receptor protein.
5. The method as claimed in claim 4, wherein “n” can be 1 or greater than 1.
6. The method as claimed in claim 1 or 2, wherein in said population, each cell expresses the same mutant variant of the receptor protein.
7. The method as claimed in claim 1 or 2, wherein said population comprises two or more sub-populations, wherein each sub-population comprises yeast cells expressing a unique mutant variant.
8. The method as claimed in claim 1 or 2, wherein said mutant variant is tethered to the cell surface.
9. The method as claimed in claim 1 or 2, wherein said cysteine specific probe is selected from the group consisting of Biotin-maleimide, Biotin-PEG2-maleimide, Biotin-PEG11-maleimide, Iodoacetic acid, Methyl methanethiosulfonate, Iodoacetamide, N-Methoxycarbonylmaleimide, Methoxy PEG Maleimide, Ellmans reagent (DTNB), TAMRA maleimide, N-(5-Fluoresceinyl)maleimide, Alexa-maleimides, Tetramethylrhodamine-maleimide, Cyanine maleimide, N-(1-Pyrenyl)maleimide, and Sulfo-Cyanine maleimide and methane thiosulfonate derivatives.
10. The method as claimed in claim 1 or 2, wherein said cysteine specific probe binds to surface exposed cysteine residues.

11. The method as claimed in claim 1 or 2, wherein said cysteine specific probe binds to non-exposed cysteine residues in presence of a denaturant.
12. The method as claimed in claim 1 or 2, wherein said molecule of interest is selected from the group consisting of antibody or fragments thereof, DNA, RNA, chemical molecule, biological molecule, peptide, polypeptide, and combinations thereof.
13. The method as claimed in claim 1 or 2, wherein said display population is selected from the group consisting of yeast display library, phage display library, mammalian display library, and lentiviral display library.
14. The method as claimed in claim 13, wherein said yeast, phage, mammalian display library, or lentiviral display population is prepared by:
a. obtaining a receptor protein;
b. creating a population of receptor protein mutant variants, wherein each mutant
variant contains a single amino acid residue mutated to a cysteine; and
c. tethering mutant variants to yeast cell, mammalian cell, phage or lentivirus
surface to obtain a surface display population.
15. The method as claimed in claim 8, wherein said population comprises yeast cells with a single type of mutant variant tethered to the cell surface.
16. The method as claimed in claim 8, wherein said population comprises at least two sub-populations, wherein each subpopulation comprises yeast cells with a single type of mutant variants tethered to yeast cell surface.
17. The method as claimed in claim 1 or claim 2, wherein the receptor protein is selected from the group consisting of CcdB antigen, HIV-1, and TA (toxin/anti-toxin) systems of Mycobacterium tuberculosis.

18. The method as claimed in claim 17, wherein the receptor protein is selected from the group consisting of HIV-1 Env, MazEF3, MazEF6, and MazEF9.
19. A yeast, phage, or lentiviral surface display library, wherein each member of the library has tethered to its surface a receptor protein mutant variant, wherein each

variant has at least a single amino acid residue mutated to an amino acid residue selected from the group consisting of cysteine or alanine or serine.
20. The library as claimed in claim 19, wherein said receptor protein has no cysteine residues, and each variant has a single mutation, wherein said mutation is a substituted cysteine, alanine and serine.
21. The library as claimed in claim 19, wherein said receptor protein has “n” number of cysteine residues involved in binding of molecule of interest, and in each mutant variant, the “n” number of cysteine residues of the receptor protein are substituted with alanine or serine, and further, an additional single substitution to cysteine is made at an amino acid position which is not any of the “n” number of cysteine residues in the receptor protein.
22. The library as claimed in claim 21, wherein “n” can be 1 or greater than 1.
23. The yeast, phage, or lentiviral surface display library as claimed in claim 19, prepared by a method comprising:
a. obtaining a receptor protein;
b. creating a population of receptor protein mutant variants, wherein each mutant
variant contains a single amino acid residue mutated to a cysteine; and
c. tethering mutant variants to yeast cell surface to obtain a yeast surface display
library.
24. The yeast, phage, or lentiviral display library as claimed in claim 19 or 20, wherein said library comprises a population of cells with a single type of mutant variant tethered to the cell surface.
25. The yeast, phage, or lentiviral display library as claimed in claim 19, wherein said library comprises at least two sub-populations, wherein each subpopulation comprises cells with a single type of mutant variant tethered to the cell surface.

Documents

Orders

Section Controller Decision Date

Application Documents

# Name Date
1 201641042053-IntimationOfGrant19-04-2023.pdf 2023-04-19
1 Form3_As Filed_08-12-2016.pdf 2016-12-08
2 201641042053-PatentCertificate19-04-2023.pdf 2023-04-19
2 Form2 Titel Page_Provisional_08-12-2016.pdf 2016-12-08
3 Drawings_As Filed_08-12-2016.pdf 2016-12-08
3 201641042053-FORM 3 [06-04-2023(online)].pdf 2023-04-06
4 Abstract_As Filed_08-12-2016.pdf 2016-12-08
4 201641042053-PETITION UNDER RULE 137 [06-04-2023(online)].pdf 2023-04-06
5 Other Patent Document [20-02-2017(online)].pdf 2017-02-20
5 201641042053-Written submissions and relevant documents [06-04-2023(online)].pdf 2023-04-06
6 Form 26 [20-02-2017(online)].pdf 2017-02-20
6 201641042053-Correspondence to notify the Controller [23-03-2023(online)].pdf 2023-03-23
7 Correspondence By Agent_Power Of Attorney_27-02-2017.pdf 2017-02-27
7 201641042053-FORM-26 [21-03-2023(online)].pdf 2023-03-21
8 201641042053-US(14)-HearingNotice-(HearingDate-23-03-2023).pdf 2023-02-23
8 201641042053-DRAWING [08-12-2017(online)].pdf 2017-12-08
9 201641042053-CORRESPONDENCE-OTHERS [08-12-2017(online)].pdf 2017-12-08
9 201641042053-EDUCATIONAL INSTITUTION(S) [12-11-2021(online)].pdf 2021-11-12
10 201641042053-CLAIMS [15-01-2021(online)].pdf 2021-01-15
10 201641042053-COMPLETE SPECIFICATION [08-12-2017(online)].pdf 2017-12-08
11 201641042053-CERTIFIED COPIES TRANSMISSION TO IB [14-12-2017(online)].pdf 2017-12-14
11 201641042053-FER_SER_REPLY [15-01-2021(online)].pdf 2021-01-15
12 201641042053-FORM 3 [14-01-2021(online)].pdf 2021-01-14
12 201641042053-Response to office action (Mandatory) [22-12-2017(online)].pdf 2017-12-22
13 201641042053-ENDORSEMENT BY INVENTORS [27-12-2017(online)].pdf 2017-12-27
13 201641042053-FER.pdf 2020-07-16
14 201641042053-FORM 3 [14-11-2019(online)].pdf 2019-11-14
14 Correspondence By Agent_Form 5_29-12-2017.pdf 2017-12-29
15 201641042053-FORM 3 [08-05-2018(online)].pdf 2018-05-08
15 201641042053-Proof of Right (MANDATORY) [23-01-2018(online)].pdf 2018-01-23
16 201641042053-FORM 18 [20-03-2018(online)].pdf 2018-03-20
16 Correspondence by Agent_Form 1_29-01-2018.pdf 2018-01-29
17 Correspondence by Agent_Form 1_29-01-2018.pdf 2018-01-29
17 201641042053-FORM 18 [20-03-2018(online)].pdf 2018-03-20
18 201641042053-FORM 3 [08-05-2018(online)].pdf 2018-05-08
18 201641042053-Proof of Right (MANDATORY) [23-01-2018(online)].pdf 2018-01-23
19 201641042053-FORM 3 [14-11-2019(online)].pdf 2019-11-14
19 Correspondence By Agent_Form 5_29-12-2017.pdf 2017-12-29
20 201641042053-ENDORSEMENT BY INVENTORS [27-12-2017(online)].pdf 2017-12-27
20 201641042053-FER.pdf 2020-07-16
21 201641042053-FORM 3 [14-01-2021(online)].pdf 2021-01-14
21 201641042053-Response to office action (Mandatory) [22-12-2017(online)].pdf 2017-12-22
22 201641042053-CERTIFIED COPIES TRANSMISSION TO IB [14-12-2017(online)].pdf 2017-12-14
22 201641042053-FER_SER_REPLY [15-01-2021(online)].pdf 2021-01-15
23 201641042053-CLAIMS [15-01-2021(online)].pdf 2021-01-15
23 201641042053-COMPLETE SPECIFICATION [08-12-2017(online)].pdf 2017-12-08
24 201641042053-EDUCATIONAL INSTITUTION(S) [12-11-2021(online)].pdf 2021-11-12
24 201641042053-CORRESPONDENCE-OTHERS [08-12-2017(online)].pdf 2017-12-08
25 201641042053-US(14)-HearingNotice-(HearingDate-23-03-2023).pdf 2023-02-23
25 201641042053-DRAWING [08-12-2017(online)].pdf 2017-12-08
26 Correspondence By Agent_Power Of Attorney_27-02-2017.pdf 2017-02-27
26 201641042053-FORM-26 [21-03-2023(online)].pdf 2023-03-21
27 Form 26 [20-02-2017(online)].pdf 2017-02-20
27 201641042053-Correspondence to notify the Controller [23-03-2023(online)].pdf 2023-03-23
28 Other Patent Document [20-02-2017(online)].pdf 2017-02-20
28 201641042053-Written submissions and relevant documents [06-04-2023(online)].pdf 2023-04-06
29 Abstract_As Filed_08-12-2016.pdf 2016-12-08
29 201641042053-PETITION UNDER RULE 137 [06-04-2023(online)].pdf 2023-04-06
30 Drawings_As Filed_08-12-2016.pdf 2016-12-08
30 201641042053-FORM 3 [06-04-2023(online)].pdf 2023-04-06
31 201641042053-PatentCertificate19-04-2023.pdf 2023-04-19
31 Form2 Titel Page_Provisional_08-12-2016.pdf 2016-12-08
32 201641042053-IntimationOfGrant19-04-2023.pdf 2023-04-19
32 Form3_As Filed_08-12-2016.pdf 2016-12-08

Search Strategy

1 searchstrategyE_27-05-2020.pdf

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