A Traditional Chinese Medicine (TCM) formula is a collection of several herbs. TCM formulae have been used to treat various diseases for several thousand years. However, wide usage of TCM formulae has results in rapid decline of some rare herbs. So it is urgent to find common available replacements for those rare herbs with the similar effects. In addition, a formula can be simplified by reducing herbs with unchanged effects. Based on this consideration, we propose a method, called “formula pair,” to replace the rare herbs and simplify TCM formulae. We show its reasonableness from a perspective of pathway enrichment analysis. Both the replacements of rare herbs and simplifications of formulae provide new approaches for a new formula discovery. We demonstrate our approach by replacing a rare herb “
Traditional Chinese Medicine is an ancient system used in disease treatments for several thousand years already [
An herb normally has five attributes: they have nature, taste, channel tropism, functions, and indications [
A formula usually contains many active compounds. These compounds target many molecules in the cell and work together to increase therapeutic efficacy and reduce adverse effects [
The availability of some herbs has a rapid decline with their wide usage [
Herb switches and simplification in a formula have been tested. For example, “Liuweidihuang” (LWDH) [
We collected 4,343 formulae and 6,171 herbs from SIRC/TCM database (
Combinational degree refers to the similarity between two formulae. The CD was calculated to evaluate combinational degree between two formulae based on the herbs they share and the weights of shared herbs. Assuming there are two formulae
The CD of
An example is shown in Table
Weight of each herb in
Formula  herb 1  herb 2  herb 3  herb 4  herb 5  herb 6  herb 7 


1  0.8  0.6  0.4  0.2  

1  0.75  0.5  0.25 
We calculated all formula pairs of 4,343 formulae. The generated values for those CDs are from 0 to 7.5; we then normalized them to
DOSim [
For a pair of formulae with a
To evaluate whether the attributes of two herbs are similar or not, a sore system was constructed for the purpose. For the five attributes in a formula, we define each one with a weight of 1. Based on a previous study, the detailed algorithms are as follows.
(1) The four natures of an herb are represented as
An example is shown in Table
Values of natures for herb
Cold  Cool  Warm  Hot  

Herb 
0.25  0.25  0.25  0.25 
Herb 
0.8  0  0  0 
(2) The five tastes are represented as
(3) The twelve channel tropisms are represented as
(4) The numbers of functions for herbs
An example is shown in Table
Functions and
Herb 
Function 1  Function 2  Function 3  Function 4  Function 5 

Herb 
Function 2  Function 4  Function 6  Function 7 
(5) The numbers of indications for herbs
So, attribute similarity (AS) of herb
If herbs
It has been a long history to use herbs to treat diseases. Herbs usually are any part of plants or certain animals with their medicinal effects. Since rare herbs decline rapidly with their wide usage, they face great threat of extinction. To protect those invaluable plants or animals, it is urgent to find the replacement for the formulae with rare herbs. Meanwhile, formulae are not changeless and can be simplified for the cost efficiency and availability. However, the prerequisites for replacements of rare herbs and simplifications of existed formulae are that the new formulae should not change the medical effects compared to original ones. According to this concept, we designed related strategy and used it to computationally detect the possibility of the replacement for all of the formulae we collected.
Combinational degree refers to the similarity of two formulae; the smaller the degree, the less similarity between two formulae. Accordingly, the formula pairs with
The replacement of herb
Herbs in SSJY, SKT, and SJZBY.
Formula  Herbs  

SJYJJS  Mulberry leaf  Chrysanthemum 

Reed rhizome 
Common hogfennel root  Bitter apricot kernel  Platycodon root  Liquorice  
SKT  Mulberry leaf  Fermented soybean  Thunberg fritillary bulb  Radix adenophorae 
White mulberry rootbark  Cape jasmine fruit  Bitter apricot kernel  Liquorice  
SJZBY  Mulberry leaf  Chrysanthemum  Thunberg fritillary bulb  Reed rhizome 
Common hogfennel root  Bitter apricot kernel  Platycodon root  Liquorice 
SSJY and SKT, meet the requirements in the replacement model based on the following results:
in SSJY,
So, we replaced “
To simplify a formula, we also built a model. For a formula pair with
Assuming formulae
if
if
if
if
if
if
Workflow of simplification.
For example, both formulae “the fifth of Du Huo Ji Sheng Tang plus/minus herbs” (FDHJST) and “Fang Feng Tang” (FFT) can treat rheumatoid arthritis (RA). FDHJST includes 15 herbs (Table
Herbs in FDHJST, FFT, and FFDHT.
Formula  Herbs  

DHJSTJJF  Root of doubleteeth pubescent angelica  Mistletoe  Radix gentianae macrophyllae 
Radix saposhnikoviae  Manchurian wildginger  Chinese angelica  
Szechwan lovage rhizome  Chinese herbaceous peony  Drying rehmannia root  
Bark of eucommia  Radix achyranthis bidentatae  Ginseng root  
Tuckahoe  Cassia bark  Liquorice  
FFT  Radix saposhnikoviae  Chinese angelica  Radix gentianae macrophyllae 
Cassia twig  Notopterygium root  Bitter apricot kernel  
Tuckahoe  Liquorice  
FFDHT  Radix saposhnikoviae  Chinese angelica  Radix gentianae macrophyllae 
Tuckahoe  Root of doubleteeth pubescent angelica  Liquorice 
To further verify that our formula replacement is relevant from biomedical view, we carried out pathway enrichment analysis with those target proteins for each formula. Protein targets of herbs in each formula were obtained from TCMID [
Top 20 pathways enriched by shared targets of SSJY and SKT with
Number  Pathway name 


1  Leishmaniasis 

2  Pathways in cancer 

3  Pertussis 

4  HTLVI infection 

5  Chagas disease (American trypanosomiasis) 

6  Tcell receptor signaling pathway 

7  Cytokines and inflammatory response 

8  Measles 

9  Legionellosis 

10  Amoebiasis 

11  Free radicalinduced apoptosis 

12  Cytokine network 

13  African trypanosomiasis 

14  IL5 signaling pathway 

15  Colorectal cancer 

16  Influence of Ras and Rho proteins on G1 to S transition 

17  NF 

18  Rheumatoid arthritis 

19  Tolllike receptor signaling pathway 

20  Signal transduction through IL1R 

Among the top 20 pathways enriched by those 78 shared targets, we found that the pathway of cytokines and inflammatory response ranked 7th and the pathway of free radicalinduced apoptosis ranked 11th. Both the two pathways were closely related to chronic bronchitis.
The results showed that there were six targets enriched in the pathway of cytokines and inflammatory response. They are granulocytemacrophage colonystimulating factor (GMCSF), tumor necrosis factor (TNF), interleukin2 (IL2), interleukin4 (IL4), interleukin6 (IL6), and interleukin10 (IL10).
Inflammation has been proved to be a central factor to the development and progression of chronic bronchitis [
Another pathway closely connected with chronic bronchitis is free radicalinduced apoptosis. It has been reported that apoptosis of structural cells in the lung may contribute to the pathogenesis of chronic bronchitis [
The new formula, SJZBY, also includes the same 78 targeted proteins. Therefore, it is reasonable to say that SJZBY should have the similar effect on the treatment of chronic bronchitis. Pathway enrichment analysis for shared targets of those formulae shows the reasonableness of this replacement.
Pathway enrichment analysis was also applied to explore the potential mechanism for formula simplification. We collected the potential targets for formulae—FDHJST, FFT, and FFDHTl; they are 182, 133, and 95 proteins, respectively. The results show that targets of FDHJST, FFT, and FFDHT are enriched in 73, 64, and 53 pathways with
Top 20 pathways enriched by targets of FDHJST with
Number  Pathway name 


1  Pathways in cancer 

2  Cytokines and inflammatory response 

3  Colorectal cancer 

4  Cytokine network 

5  Malaria 

6  Chagas disease (American trypanosomiasis) 

7  Pancreatic cancer 

8  Amoebiasis 

9  Bladder cancer 

10  Leishmaniasis 

11  Pertussis 

12  Tuberculosis 

13  Legionellosis 

14  Rheumatoid arthritis 

15  Small cell lung cancer 

16  Chronic myeloid leukemia 

17  Prostate cancer 

18  HTLVI infection 

19  Influenza A 

20  African trypanosomiasis 

Top 20 pathways enriched by targets of FFT with
Number  Pathway name 


1  Pathways in cancer 

2  Colorectal cancer 

3  Cytokines and inflammatory response 

4  Cytokine network 

5  Prostate cancer 

6  Amoebiasis 

7  Pancreatic cancer 

8  Chagas disease (American trypanosomiasis) 

9  Chronic myeloid leukemia 

10  Pertussis 

11  Leishmaniasis 

12  Apoptotic signaling in response to DNA damage 

13  Tuberculosis 

14  Small cell lung cancer 

15  Influence of Ras and Rho proteins on G1 to S Transition 

16  p53 signaling pathway 

17  Toxoplasmosis 

18  Measles 

19  Malaria 

20  HTLVI infection 

Pathways enriched by targets of FFDHT with
Number  Pathway name 


1  Pathways in cancer 

2  Colorectal cancer 

3  Prostate cancer 

4  p53 signaling pathway 

5  Pertussis 

6  Small cell lung cancer 

7  Influence of Ras and Rho proteins on G1 to S transition 

8  Endometrial cancer 

9  Pancreatic cancer 

10  Amyotrophic lateral sclerosis (ALS) 

11  Cytokines and inflammatory response 

12  Bladder cancer 

13  Tuberculosis 

14  Amoebiasis 

15  Apoptosis 

16  HTLVI infection 

17  Cytokine network 

18  RB tumor suppressor/checkpoint signaling in response to DNA damage 

19  Apoptotic signaling in response to DNA damage 

20  Chronic myeloid leukemia 

In those top 20 pathways enriched by targets of FDHJST, we found that the pathway of cytokines and inflammatory response were closely connected with RA. The result showed that the
A previous report has confirmed that antagonism of GMCSF represents a novel therapeutic approach for a variety of autoimmunemediated inflammatory diseases, including RA [
For those interleukins, IL6 and IL8 can be found in RA pathway in KEGG pathway annotation [
Among those top 20 enriched pathways by targets of FFT, the pathway of cytokines and inflammatory response was closely connected with RA. The result showed that this pathway ranked third among the top 20 pathways according the
After simplification, the resulting new formula, FFDHT, was also enriched in the pathway of cytokines and inflammatory response with the
Many herbs used in Traditional Chinese Medicine are endangered, such as tiger bone used to treat rheumatism. Its widely usage results in the rapid decline of tigers with the poaching and illegal trade, which push tigers to extinction [
Moreover, we also proposed a method to simplify formulae based on the similar rationale. A new formula can be formulated with “less herbs but same effect” concept to the original one. Pathway enrichment analysis also shows the reasonableness of the simplification. Our approaches provide an alternative way to reformulate those traditional prescriptions.
Although herbs have been widely used for thousands of years, most of their targets are still unclear and the mechanisms underling their effects remain unknown. And that has strongly prevented the modernization of traditional Chinese Medicine. For example, in the method of score system of attributes’ similarities for herb pairs, we found that “rhinoceros horn” and “Buffalo Horn” have high attributes’ similarity (
In this work, both replacement of rare herbs and simplification of formulae were computationally tested; our approaches provide an alternative way for new TCM formulation and mechanism inference. To fully verify our method and test the effects of those new formulae, more preclinical experiments need to be conducted. By the combination of
The authors are grateful to Ms. Bingxing Lu for her help in paper preparation. This work was supported by the National 973 Key Basic Research Program (Grant no. 2010CB945401 and 2012CB910400), the National Natural Science Foundation of China (Grant no. 31171264, 31071162, 31000590, and 81171272), and the Science and Technology Commission of Shanghai Municipality (11DZ2260300).