# US 2014/0195216 A1 · Computational design of ideotypically modulated pharmacoeffectors for selective cell treatment

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- Number: US 2014/0195216 A1
- Document ID: US20140195216A1
- Status: Published application
- Kind: A1
- Application number: 13/736,797
- Filed: 2013-01-08
- Published: 2014-07-10
- Earliest claimed: 2013-01-08
- Assignees: Imperium Biotechnologies, Inc.
- Applicants: Imperium Biotechnologies, Inc.
- Inventors: Jacob Jennings Orme
- Web page: https://patentgrep.com/patent/US20140195216A1

## CPC

- G16B 20/00: ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
- G16B: BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY

## Abstract

In system and method embodiments, an embodiment includes the collection, input, and organization of target nucleotide source or sources; the identification of potential target sequences for ideotypically modulated pharmacoeffectors (IMP); the exclusion, prioritization, or deprioritization of target sequences on the basis of undesirable binding for ideotypically modulated pharmacoeffectors (IMP); and/or the design of targeting sequences on the basis of reverse complementarity or sequence complementarity. IMPs are designed for optimal use in respective applications, including cancers, autoimmune diseases, infectious diseases, cellular diseases, and other applications.

## Claims

### Claim 1

A system when executed comprising two or more of the following steps:
the collection, input, and organization of target nucleotide source or sources;
the identification of potential target sequences for ideotypically modulated pharmacoeffectors (IMP);
the exclusion, prioritization, or deprioritization of target sequences on the basis of undesirable binding for ideotypically modulated pharmacoeffectors (IMP); or
the design of targeting sequences on the basis of reverse complementarity or sequence affinity.

### Claim 2 (depends on 1)

The system of claim 1, wherein said target nucleotide source(s) comprise viral, cancerous, bacterial, MHC, transplant-related, disease-causing, or of-interest cellular material.

### Claim 3 (depends on 1)

The system of claim 1, wherein cancerous, autoimmune, transplant-related, or other cells are sequenced in order to provide said target nucleotide source or sources.

### Claim 4 (depends on 1)

The system of claim 1, wherein cells of interest are expanded or proliferated prior to sequencing to provide said target nucleotide source or sources.

### Claim 5 (depends on 1)

The system of claim 1, wherein sequences are aligned and/or sequences are compiled to a consensus sequence.

### Claim 6 (depends on 1)

The system of claim 1, wherein said potential target sequences are determined using user-defined parameters and one or more search algorithm(s).

### Claim 7 (depends on 1)

The system of claim 1, wherein said undesirable binding evaluation is performed using NCBI BLAST© software.

### Claim 8 (depends on 1)

The system of claim 1, wherein said undesirable binding evaluation is performed using thermodynamic calculations.

### Claim 9 (depends on 1)

The system of claim 1, wherein said potential target sequences are evaluated theoretically.

### Claim 10 (depends on 1)

The system of claim 1, wherein said potential target sequences are evaluated physically.

### Claim 11 (depends on 1)

The system of claim 1, wherein IMPs are designed with gaps of multiples of 9, 10, or 11 base pairs.

### Claim 12 (depends on 1)

The system of claim 1, wherein IMPs are designed to avoid hairpin structures.

### Claim 13 (depends on 1)

The system of claim 1, wherein IMPs are designed to avoid high-mutation sites.

### Claim 14 (depends on 1)

The system of claim 1, wherein IMPs are designed with “wobble” sites.

### Claim 15 (depends on 1)

The system of claim 1, wherein some or all functions are performed using a computer.

### Claim 16 (depends on 1)

The system of claim 1, wherein some or all functions are performed by a human being.