Peptide Studio



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Peptide Studio

Physiologically active peptide design services to reduce the time and effort of researchers to the utmost and to offer better outcomes

The PH method (Protein & Hit Method), an algorithm that PH Japan has developed, is capable of providing the following services:

Sequence optimization by amino acid substitution

Based on the hypothesis that cell-adhesive peptide GRGDS is an unknown sequence and if you have a sequence of either GRGD or GRGDG, our service can offer the design of GRGDS, WRGDVV, HRGDAT and ARGDMCS, for example.

Service for designing physiologically active peptides

Our service offers the design of sequences which allow the prediction of activities and effects using approximately 5 residues as the lead sequence with up to roughly 30 residues.

Principle of PH method


This section explains cell-adhesive peptide, GRGDS, taking wooden blocks as an example.
After processing with the PH method algorithm, the peptide will look like the drawing.

Symmetry is achieved when blocks of structurally different amino acids are sequenced in an orderly manner in the proper height. The peptide sequence in this symmetric state is estimated to have some activities.

Our design service begins with, for example, 15 residues of physiologically active peptides. The design uses approximately 5 or more residues at the N terminal side as the lead sequence. In this design, the sequence does not have the top block S as in the drawing, and the sequence has a symmetry break.

Still, the axis direction remains the same. This means that the activity axis is fixed to a certain degree.
Our design service continues to add amino acids along the axis to reach an appropriate sequence length. In this process, multiple amino acid candidates may arise. This is a point where amino acids can be substituted.

More specific explanations are provided below using angiotensin as an example.

There are two types of elements that can be physiologically active peptides.

Element A: In an appropriate amino acid sequence
Element B: In an appropriate sequence length

Angiotensin I: Asp - Arg - Val - Tyr - Ile - His - Pro - Phe - His- Leu - OH
Angiotensin II: Asp- Arg - Val - Tyr - Ile - His - Pro - Phe - OH

Angiotensin II, which is recognized to have the most hypertensive effect, satisfies both Elements A and B.
Angiotensin I, which does not produce a hypertensive effect, has redundant residues of His - Leu at the C terminal side.

Angiotensin I is like redundant amino acid blocks being piled up on the wooden blocks shown in the drawing, causing a symmetry break.

Angiotensin I satisfies Element A but fails for Element B. In this case, peptide activities are significantly compromised or even lost.

For an example design, Asp -Arg - Val - Tyr on the N-terminal side is used as the lead sequence, but amino acids from the 5th residue are removed. In this case, the sequence does not meet the criteria for Element B but satisfies Element A, which may indicate that the activity axis is somewhat fixed to a certain degree.

The designs below involve repeating sequencing from the N terminal to the C terminal side or from the C terminal to the N terminal side, where the direction of activities may reach an area of antagonists.

Using Asp - Arg - Val - Tyr at the N terminal side as the lead sequence, not only angiotensin II: Asp - Arg - Val - Tyr - Ile - His - Pro – Phe but also its receptor antagonist (CH3-Gly Arg Val Tyr Val His Pro Ala ) are known as physiologically active substances. The following show the design of some sequences containing these sequences:

Asp- Arg - Val - Tyr - Ile - His - Pro - Phe (DRVYIHPF): Angiotensin II
Gly Arg Val Tyr Val His Pro Ala (GRVYVHPA): A structure similar to angiotensin II antagonist
Asp- Arg - Val - Tyr - Ile - His - Pro - Tyr (DRVYIHPY)
Lys- Arg-Met-Val- Tyr- Val-His- Pro - Ala (KRMVYVHPA)
Asp- Arg- Val-Tyr- Gln-Met-Gln (DRVYQMQ)

The following are other examples:
Based on the known sequence of CYFQNCPRG-NH2 (Disulfide bridge: 1-6), CYFQNC is used as the lead sequence to design two types of sequences as shown below:

CYFQNCPRG-NH2 (Disulfide bridge: 1 - 6)
CYFQNCPYQGY-NH2 (Disulfide bridge: 1 - 6)

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