Computer-assisted design of anti-peptides based on the amino acid sequence of a target peptide
First Claim
1. A method of purifying a target polypeptide or a fragment thereof, comprising(1) designing an anti-peptide sequence having high affinity and specificity for a target peptide or a fragment thereof contained in said polypeptide by(I) obtaining an amino acid sequence Pi of the target peptide or a fragment thereof
(II) entering into a computer said amino acid sequence as a first array;
(III) obtaining from a first data base a first hydropathic value for each member of the first array
space="preserve" listing-type="equation">h.sub.1 -h.sub.2 -h.sub.3 -. . . -h.sub.n ;
(IV) storing within the computer said first hydropathic values as a second array;
(V) summing the values in said second array to obtain a value ai for a first moving average hydropathy ai for each member of the first array in accordance with ##EQU12## wherein k is (i-S) to (i+S),i is greater than S and up to or equal to (n-S),S is (r-1)/2,r is an odd numeral up to or equal to n, andn is the number of amino acids in the sequence or fragment thereof;
(VI) storing said values for the first moving average hydropathy in the computer as a third array;
(VII) obtaining from a second anti-sense or hydropathically complementary amino acid data base a set comprising at least one anti-sense amino acid per member of the first array;
(VIII) storing within the computer said sets of at least one anti-sense amino acid as a fourth array;
(IX) generating with the computer at least one anti-sense amino acid sequence by selecting one member Qj,i per set in the fourth array
space="preserve" listing-type="equation">Q.sub.j,i =Q.sub.j,1 -Q.sub.j,2 -Qj,3-. . . -Q.sub.j,n'"'"' ;
(X) storing within the computer said at least one anti-sense amino acid sequence as a fifth array;
(XI) obtaining from the first data base a second hydropathic value hj,i for each member of the fifth array
space="preserve" listing-type="equation">h'"'"'.sub.j,i -h'"'"'.sub.j,2 -h'"'"'.sub.j,3 -. . . -h'"'"'.sub.j,n '"'"';
(XII) storing within the computer said second hydropathic values as a sixth array;
(XIII) summing the values in said sixth array to obtain a value bj,i for a second moving average hydropathy for each member of the fifth array in accordance with ##EQU13## wherein K is (i-S) to (i+S),i is greater than S and up to or equal to (n-S),j is 1 to the total number of sequences in the fifth array,S is (r-1)/2,r is an odd numeral up to or equal to n, and peptide sequence or fragment thereof;
(XIV) storing said second average hydropathy values in the computer as a seventh array;
(XV) generating within the computer one hydropathic complementary score θ
j for each anti-peptide sequence or fragment thereof in the fifth array in accordance with
space="preserve" listing-type="equation">θ
.sub.j =((Σ
(a.sub.k +b.sub.j,k).sup.2)/(n-2S)).sup.1/2,whereinK is (S+1) to (n-S), andn and S are as defined above;
(XVI) storing within the computer the hydropathic complementary scores as an eighth array;
(XVII) identifying within the eighth array a group having a lowest score;
(XVIII) identifying and selecting the at least one anti-sense sequence in the fifth array which corresponds to said at least one lowest score and identifying it as the at least one anti-peptide sequence having high affinity and selectivity for the target peptide or fragment thereof(2) synthesizing an anti-[poly]peptide comprising the anti-peptide sequence;
(3) contacting said synthesized anti-peptide with a sample comprising the target polypeptide to promote binding therebetween;
(4) separating said polypeptide-bound anti-peptide from the remaining components in the sample; and
(5) separating said peptide from the anti-peptide.
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Accused Products
Abstract
A computer-implemented method for designing at least one anti-peptide sequence having affinity for target peptide or a fragment thereof suitable for synthesizing peptides and micromolecules, assaying for a target peptides, purifying target peptides, and/or preventing proteolyis of a polypeptide includes identification of the members of the amino acid sequence of the target peptide and their anti-sense or hydropathically complementary amino acids and determining the moving average hydropathy for the target and anti-sense members. The resulting lowest hydropathy identifies the anti-sense amino acid sequence for the target peptide. The members of the target peptide amino acid sequence are obtained along with their member-specific hydropathic values with the hydropathic values summed as a moving average. Anti-sense or complementary amino acid members are identified from the moving average information to generate an array of anti-sense amino acid sequences. The hydropathic values of the array of anti-sense amino acids are obtained along with their moving average hydropathic values from which a hydropathic complementary score is obtained with the lowest score identifying the anti-sense amino acid sequence having affinity for the target peptide.
122 Citations
30 Claims
- 1. A method of purifying a target polypeptide or a fragment thereof, comprising
(1) designing an anti-peptide sequence having high affinity and specificity for a target peptide or a fragment thereof contained in said polypeptide by (I) obtaining an amino acid sequence Pi of the target peptide or a fragment thereof - space="preserve" listing-type="equation">P.sub.i =P.sub.1 -P.sub.2 -P.sub.3 -. . . -P.sub.h ;
(II) entering into a computer said amino acid sequence as a first array; (III) obtaining from a first data base a first hydropathic value for each member of the first array
space="preserve" listing-type="equation">h.sub.1 -h.sub.2 -h.sub.3 -. . . -h.sub.n ;(IV) storing within the computer said first hydropathic values as a second array; (V) summing the values in said second array to obtain a value ai for a first moving average hydropathy ai for each member of the first array in accordance with ##EQU12## wherein k is (i-S) to (i+S), i is greater than S and up to or equal to (n-S), S is (r-1)/2, r is an odd numeral up to or equal to n, and n is the number of amino acids in the sequence or fragment thereof; (VI) storing said values for the first moving average hydropathy in the computer as a third array; (VII) obtaining from a second anti-sense or hydropathically complementary amino acid data base a set comprising at least one anti-sense amino acid per member of the first array; (VIII) storing within the computer said sets of at least one anti-sense amino acid as a fourth array; (IX) generating with the computer at least one anti-sense amino acid sequence by selecting one member Qj,i per set in the fourth array
space="preserve" listing-type="equation">Q.sub.j,i =Q.sub.j,1 -Q.sub.j,2 -Qj,3-. . . -Q.sub.j,n'"'"' ;(X) storing within the computer said at least one anti-sense amino acid sequence as a fifth array; (XI) obtaining from the first data base a second hydropathic value hj,i for each member of the fifth array
space="preserve" listing-type="equation">h'"'"'.sub.j,i -h'"'"'.sub.j,2 -h'"'"'.sub.j,3 -. . . -h'"'"'.sub.j,n '"'"';(XII) storing within the computer said second hydropathic values as a sixth array; (XIII) summing the values in said sixth array to obtain a value bj,i for a second moving average hydropathy for each member of the fifth array in accordance with ##EQU13## wherein K is (i-S) to (i+S), i is greater than S and up to or equal to (n-S), j is 1 to the total number of sequences in the fifth array, S is (r-1)/2, r is an odd numeral up to or equal to n, and peptide sequence or fragment thereof; (XIV) storing said second average hydropathy values in the computer as a seventh array; (XV) generating within the computer one hydropathic complementary score θ
j for each anti-peptide sequence or fragment thereof in the fifth array in accordance with
space="preserve" listing-type="equation">θ
.sub.j =((Σ
(a.sub.k +b.sub.j,k).sup.2)/(n-2S)).sup.1/2,wherein K is (S+1) to (n-S), and n and S are as defined above; (XVI) storing within the computer the hydropathic complementary scores as an eighth array; (XVII) identifying within the eighth array a group having a lowest score; (XVIII) identifying and selecting the at least one anti-sense sequence in the fifth array which corresponds to said at least one lowest score and identifying it as the at least one anti-peptide sequence having high affinity and selectivity for the target peptide or fragment thereof (2) synthesizing an anti-[poly]peptide comprising the anti-peptide sequence; (3) contacting said synthesized anti-peptide with a sample comprising the target polypeptide to promote binding therebetween; (4) separating said polypeptide-bound anti-peptide from the remaining components in the sample; and (5) separating said peptide from the anti-peptide. - View Dependent Claims (2, 3, 4, 5)
- space="preserve" listing-type="equation">P.sub.i =P.sub.1 -P.sub.2 -P.sub.3 -. . . -P.sub.h ;
- 6. A method of preventing proteolysis of a polypeptide in the presence of a proteolytic enzyme, comprising
(1) designing an anti-peptide having high affinity and specificity for a target peptide or fragment thereof contained in the polypeptide by (I) obtaining an amino acid sequence Pi of the target peptide or a fragment thereof - space="preserve" listing-type="equation">P.sub.i =P.sub.1 -P.sub.2 -P.sub.3 -. . . -P.sub.h ;
(II) entering into a computer said amino acid sequence as a first array; (III) obtaining from a first data base a first hydropathic value for each member of the first array
space="preserve" listing-type="equation">h.sub.1 -h.sub.2 -h.sub.3 -. . . -h.sub.n ;(IV) storing within the computer said first hydropathic values as a second array; (V) summing the values in said second array to obtain a value ai for a first moving average hydropathy ai for each member of the first array in accordance with ##EQU14## wherein k is (i-S) to (i+S), i is greater than S and up to or equal to (n-S), S is (r-1)/2, r is an odd numeral up to or equal to n, and n is the number of amino acids in the sequence or fragment thereof; (VI) storing said values for the first moving average hydropathy in the computer as a third array; (VII) obtaining from a second anti-sense or hydropathically complementary amino acid data base a set comprising at least one anti-sense amino acid per member of the first array; (VIII) storing within the computer said sets of at least one anti-sense amino acid as a fourth array; (IX) generating with the computer at least one anti-sense amino acid sequence by selecting one member Qj,i per set in the fourth array
space="preserve" listing-type="equation">Q.sub.j,i =Q.sub.j,1 -Q.sub.j,2 -Qj,3-. . . -Q.sub.j,n'"'"' ;(X) storing within the computer said at least one anti-sense amino acid sequence as a fifth array; (XI) obtaining from the first data base a second hydropathic value hj,i for each member of the fifth array
space="preserve" listing-type="equation">h'"'"'.sub.j,i -h'"'"'.sub.j,2 -h'"'"'.sub.j,3 -. . . -h'"'"'.sub.j,n '"'"';(XII) storing within the computer said second hydropathic values as a sixth array; (XIII) summing the values in said sixth array to obtain a value bj,i for a second moving average hydropathy for each member of the fifth array in accordance with ##EQU15## wherein K is (i-S) to (i+S), i is greater than S and up to or equal to (n-S), j is 1 to the total number of sequences in the fifth array, S is (r-1)/2, r is an odd numeral up to or equal to n, and n is the number of amino acids in the anti-peptide sequence or fragment thereof; (XIV) storing said second average hydropathy values in the computer as a seventh array; (XV) generating within the computer one hydropathic complementary score θ
j for each anti-peptide sequence or fragment thereof in the fifth array in accordance with ##EQU16## wherein K is (S+1) to (n-S), andn and S are as defined above; (XVI) storing within the computer the hydropathic complementary scores as an eighth array a group having a lowest score; (XVII) identifying within the eighth array a group having a lowest score; (XVIII) identifying and selecting the at least one anti-sense sequence in the fifth array which corresponds to said at least one lowest score and identifying it as the at least one anti-peptide sequence having high affinity and selectivity for the target peptide or fragment thereof (2) synthesizing an anti-polypeptide comprising the anti-peptide sequence; and (3) contacting said anti-polypeptide with a sample comprising the target polypeptide to promote binding therebetween, to thereby protect the polypeptide and prevent the proteolysis thereof when placed in contact with a proteolytic enzyme. - View Dependent Claims (7, 8, 9)
- space="preserve" listing-type="equation">P.sub.i =P.sub.1 -P.sub.2 -P.sub.3 -. . . -P.sub.h ;
- 10. A method of preventing or reducing the binding of a first polypeptide or fragments thereof having affinity for a target peptide to a second polypeptide comprising said target peptide, comprisingdesigning an anti-peptide sequence having affinity for the target peptide or a fragment thereof by
(I) obtaining an amino acid sequence Pi of the target peptide or a fragment thereof - space="preserve" listing-type="equation">P.sub.i =P.sub.1 -P.sub.2 -P.sub.3 -. . . -P.sub.h ;
(II) entering into a computer said amino acid sequence as a first array; (III) obtaining from a first data base a first hydropathic value for each member of the first array
space="preserve" listing-type="equation">h.sub.1 -h.sub.2 -h.sub.3 -. . . -h.sub.n ;(IV) storing within the computer said first hydropathic values as a second array; (V) summing the values in said second array to obtain a value ai for a first moving average hydropathy ai for each member of the first array in accordance with ##EQU17## wherein k is (i-S) to (i+S), i is greater than S and up to or equal to (n-S), S is (r-1)/2, r is an odd numeral up to or equal to n, and n is the number of amino acids in the sequence or fragment thereof; (VI) storing said values for the first moving average hydropathy in the computer as a third array; (VII) obtaining from a second anti-sense or hydropathically complementary amino acid data base a set comprising at least one anti-sense amino acid per member of the first array; (VIII) storing within the computer said sets of at least one anti-sense amino acid as a fourth array; (IX) generating with the computer at least one anti-sense amino acid sequence by selecting one member Qj,i per set in the fourth array
space="preserve" listing-type="equation">Q.sub.j,i =Q.sub.j,1 -Q.sub.j,2 -Qj,e-. . . -Q.sub.j,n'"'"' ;(X) storing within the computer said at least one anti-sense amino acid sequence as a fifth array; (XI) obtaining from the first data base a second hydropathic value hj,i for each member of the fifth array
space="preserve" listing-type="equation">h'"'"'.sub.j,i -h'"'"'.sub.j,2 -h'"'"'.sub.j,3 -. . . -h'"'"'.sub.j,n '"'"';(XII) storing within the computer said second hydropathic values as a sixth array; (XIII) summing the values in said sixth array to obtain a value bj,i for a second moving average hydropathy for each member of the fifth array in accordance with ##EQU18## wherein K is (i-S) to (i+S), i is greater than S and up to or equal to (n-S), j is 1 to the total number of sequence in the fifth array, S is (r-1)/2, r is an odd numeral up to or equal to n, and peptide sequence or fragment thereof; (XIV) storing said second average hydropathy values in the computer as a seventh array; (XV) generating within the computer one hydropathic complementary score θ
j for each anti-peptide sequence or fragment thereof in the fifth array in accordance with
space="preserve" listing-type="equation">θ
.sub.j =((Σ
(a.sub.k +b.sub.j,k).sup.2)/(n-2S)).sup.1/2,wherein K is (S+1) to (n-S), and n and S are as defined above; (XVI) storing within the computer the hydropathic complementary scores as an eighth array; (XVII) identifying within the eighth array a group having a lowest score; (XVIII) identifying and selecting the at least one anti-sense sequence in the fifth array which corresponds to said at least one lowest score and identifying it as the at least one anti-peptide sequence having high affinity and selectivity for the target peptide or fragment thereof (2) synthesizing an anti-polypeptide comprising said anti-peptide sequence; and (3) contacting said anti-polypeptide with a sample comprising said second polypeptide to promote binding therebetween to thereby prevent or reduce the binding of said second polypeptide to said first polypeptide in the presence thereof. - View Dependent Claims (11, 12, 13)
- space="preserve" listing-type="equation">P.sub.i =P.sub.1 -P.sub.2 -P.sub.3 -. . . -P.sub.h ;
- 14. A method of assaying for a target peptide or a fragment thereof, comprising
(1) designing an anti-peptide sequence having affinity for a target peptide or a fragment thereof contained in the polypeptide by (I) obtaining an amino acid sequence Pi of the target peptide or a fragment thereof - space="preserve" listing-type="equation">P.sub.i =P.sub.1 -P.sub.2 -P.sub.3 -. . . -P.sub.h ;
(II) entering into a computer said amino acid sequence as a first array; (III) obtaining from a first data base a first hydropathic value for each member of the first array
space="preserve" listing-type="equation">h.sub.1 -h.sub.2 -h.sub.3 -. . . -h.sub.n ;(IV) storing within the computer said first hydropathic values as a second array; (V) summing the values in said second array to obtain a value ai for a first moving average hydropathy ai for each member of the first array in accordance with ##EQU19## wherein k is (i-S) to (i+S), i is greater than S and up to or equal to (n-S), S is (r-1)/2, r is an odd numeral of amino acids in the sequence or fragment thereof; n is the number of amino acids in the sequence or fragment thereof; (VI) storing said values for the first moving average hydropathy in the computer as a third array; (VII) obtaining from a second anti-sense or hydropathically complementary amino acid data base a set comprising at least one anti-sense amino acid per member of the first array; (VIII) storing within the computer said sets of at least one anti-sense amino acid as a fourth array; (IX) generating with the computer at least one anti-sense amino acid sequence by selecting one member Qj,i per set in the fourth array
space="preserve" listing-type="equation">Q.sub.j,i =Q.sub.j,1 -Q.sub.j,2 -Qj,3-. . . -Q.sub.j,n'"'"' ;(X) storing within the computer said at least one anti-sense amino acid sequence as a fifth array; (XI) obtaining from the first data base a second hydropathic value hj,i for each member of the fifth array
space="preserve" listing-type="equation">h'"'"'.sub.j,i -h'"'"'.sub.j,2 -h'"'"'.sub.j,3 -. . . -h'"'"'.sub.j,n '"'"';(XII) storing within the computer said second hydropathic values as a sixth array; (XIII) summing the values in said sixth array to obtain a value bj,i for a second moving average hydropathy for each member of the fifth array in accordance with ##EQU20## wherein K is (i-S) to (i+S), i is greater than S and up to or equal to (n-S), j is 1 to the total number of sequences in the fifth array, S is (r-1)/2, r is an odd numeral up to or equal to n, and n is the number of amino acids in the anti-peptide sequence or fragment thereof; (XIV) storing said second average hydropathy values in the computer as a seventh array; (XV) generating within the computer one hydropathic complementary score θ
j for each anti-peptide sequence or fragment thereof in the fifth array in accordance with
space="preserve" listing-type="equation">θ
.sub.j =((Σ
(a.sub.k +b.sub.j,k).sup.2)/(n-2S)).sup.1/2,wherein K is (s+1) to (n-S), and n and S are as defined above; (XVI) storing within the computer the hydropathic complementary scores as an eighth array; (XVII) identifying within the eighth array a group having a lowest score; (VIII) identifying and selecting the at least one anti-sense sequence in the fifth array which corresponds to said at least one lowest score and identifying it as the at least one anti-peptide sequence having high affinity and selectivity for the target peptide or fragment thereof (2) synthesizing an anti-polypeptide comprising the anti-peptide sequence; (3) contacting said anti-polypeptide with a sample comprising the target polypeptide to promote binding; and (4) determining the presence of said polypeptide-bound antipolypeptide. - View Dependent Claims (15, 16, 17, 18, 19, 20, 21)
- space="preserve" listing-type="equation">P.sub.i =P.sub.1 -P.sub.2 -P.sub.3 -. . . -P.sub.h ;
- 22. A method of synthesizing an anti-peptide macromolecule having affinity for a target peptide or a fragment thereof, comprising
(1) designing an anti-peptide sequence having high affinity and specificity for a target peptide or a fragment thereof contained in the polypeptide by (I) obtaining an amino acid sequence Pi of the target peptide or a fragment thereof - space="preserve" listing-type="equation">P.sub.i =P.sub.1 -P.sub.2 -P.sub.3 -. . . -P.sub.h ;
(II) entering into a computer said amino acid sequence as a first array; (III) obtaining from a first data base a first hydropathic value for each member of the first array
space="preserve" listing-type="equation">h.sub.1 -h.sub.2 -h.sub.3 -. . . -h.sub.n ;(IV) storing within the computer said first hydropathic values as a second array; (V) summing the values in said second array to obtain a value ai for a first moving average hydropathy ai for each member of the first array in accordance with ##EQU21## wherein k is (i-S) to (i+S), i is greater than S and up to or equal to (n-S), S is (r-1)/2, r is an odd numeral up to or equal to n, and n is the number of amino acids in the sequence or fragment thereof; (VI) storing said values for the first moving average hydropathy in the computer as a third array; (VII) obtaining from a second anti-sense or hydropathically complementary amino acid data base a set comprising at least one anti-sense amino acid per member of the first array; (VIII) storing within the computer said sets of at least one anti-sense amino acid as a fourth array; (IX) generating with the computer at least one anti-sense amino acid sequence by selecting one member Qj,i per set in the fourth array
space="preserve" listing-type="equation">Q.sub.j,i =Q.sub.j,1 -Q.sub.j,2 -Qj,3 -. . . -Q.sub.j,n'"'"' ;(X) storing within the computer said at least one anti-sense amino acid sequence as a fifth array; (XI) obtaining from the first data base a second hydropathic value hj,i for each member of the fifth array
space="preserve" listing-type="equation">h'"'"'.sub.j,i -h'"'"'.sub.j,2 -h'"'"'.sub.j,3 -. . . -h'"'"'.sub.j,n '"'"';(XII) storing within the computer said second hydropathic values as a sixth array; (XIII) summing the values in said sixth array to obtain a value bj,i for a second moving average hydropathy for each member of the fifth array in accordance with ##EQU22## wherein K is (i-S) to (i+S), i is greater than S and up to or equal to (n-S), j is 1 to the total number of sequences in the fifth array, S is (r-1)/2, r is an odd numeral up to or equal to n, and n is the number of amino acids in the anti-peptide sequence or fragment thereof; (XV) generating within the computer one hydropathic complementary score θ
j for each anti-peptide sequence or fragment thereof in the fifth array in accordance with
space="preserve" listing-type="equation">θ
.sub.j =((Σ
(a.sub.k +b.sub.j,k).sup.2)/(n-2S)).sup.1/2,wherein K is (S+1) to (n-S), and n and S are as defined above; (XVI) storing within the computer the hydropathic complementary scores as an eighth array; (XVII) identifying within the eighth array a group having a lowest score; (XVIII) identifying and selecting the at least one anti-sense sequence in the fifth array which corresponds to said at least one lowest score and identifying it as the at least one anti-peptide sequence having high affinity and selectivity for the target peptide or fragment thereof (2) synthesizing an anti-polypeptide comprising the anti-peptide sequence; (3) covalently binding at least two molecules of said anti-polypeptide to obtain said macromolecule. - View Dependent Claims (23, 24, 25, 26, 27, 28, 29, 30)
- space="preserve" listing-type="equation">P.sub.i =P.sub.1 -P.sub.2 -P.sub.3 -. . . -P.sub.h ;
Specification
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- Resources
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Current AssigneeUnited States Department Of Health And Human Services
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Original AssigneeGovernment of the United States of America
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InventorsFassina, Giorgio, Olson, Arthur D., Omichinski, James G., Thorgeirsson, Snorri S.
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Primary Examiner(s)Teska, Kevin J.
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Application NumberUS07/322,266Time in Patent Office1,037 DaysField of Search364/496, 364/497, 364/413.01, 435/69.1, 435/68.1, 435/69.4, 436/508, 436/89, 935/77, 935/78, 935/87US Class Current703/6CPC Class CodesC07K 1/00 General methods for the pre...G01N 33/68 involving proteins, peptide...
