How easy is it to synthesize a drug on the market?

Introduction

Therefore, a useful index called ** SA score ** that can be used with RDKit [^ 1].

From the result

--Average: 3.5 --Median: 3.1

sascore_hist.png It would be helpful when narrowing down candidate compounds using the SA score as a guide.

Preprocessing

--2020-04-07 Medical drugs currently manufactured and sold in Japan -KEGG DRUG with D number assigned drugs (2826 types, duplicates) --Desalting because I want to see the ease of synthesis of the main fragments --I borrowed @ yamasakih's desalt.py [^ 2] [^ 2]: Commentary; The story of creating a compound database that can be accessed from Jupyter Notebook for drug discovery raid battle 2018 with Docker-compose of razi --Qiita --Calculate SA score

Calculation

This time, we will focus on compounds with 2 or more carbon atoms. In addition, mixed drugs, non-medicinal drugs, blood products, antibody drugs, crude drugs, etc. are excluded because they do not meet the purpose. The narrowing down at this point is 1641 compounds. Since the ones classified into multiple medicinal effects are duplicated, they are deleted to make 1436 compounds. The histogram will be the one described above.

mean std min 25% 50% 75% max
3.472627 1.262086 1.054917 2.547814 3.14387 4.190424 9.129873

Try to divide by medicinal effect classification

The overall distribution is found above. There is also information on drug efficacy classification, so let's see if there are any differences. Here, the calculation is based on the 1641 compound with no duplicates removed.

Drugs for the nervous system and sensory organs

Furthermore, it is classified into central nervous system drugs, peripheral nervous system drugs, sensory organ drugs, and others. Memantine and baclofen belong to the drug.

count mean std min 25% 50% 75% max
401 3.074675 1.066451 1.407299 2.368182 2.79175 3.496406 8.224301

1_神経系及び感覚器官用医薬品.png

Individual organ system medicines

Furthermore, it is classified into circulatory organ medicine, respiratory organ medicine, digestive organ medicine, hormonal medicine, urinary and reproductive organ and anal medicine, dermal medicine, dental and oral medicine, and others. Examples of pharmaceuticals include olmesartan and esomeprazole.

count mean std min 25% 50% 75% max
567 3.436648 1.211883 1.176561 2.556412 3.073396 4.338626 9.129873

2_個々の器官系用医薬品.png

Metabolic drugs

Furthermore, it is classified into vitamins, nourishing tonics, blood fluids, dialysis drugs, and others. Pharmaceuticals include prasugrel and canagliflozin.

count mean std min 25% 50% 75% max
196 3.562633 1.263028 1.58004 2.774178 3.307104 4.199926 9.121023

3_代謝性医薬品.png

Drugs for tissue cell function

Furthermore, it is classified into cell-utilizing drugs, tumor drugs, radiopharmaceuticals, allergy drugs, and others. Drugs include irinotecan and cetirizine.

count mean std min 25% 50% 75% max
191 3.608295 1.438333 1.694618 2.641493 3.066941 4.15542 7.705978

4_組織細胞機能用医薬品.png

Crude drugs and medicines based on Chinese prescription

Not applicable.

Drugs for pathogenic organisms

Furthermore, it is classified into antibiotic preparations, chemotherapeutic agents, biologics, parasite drugs, and others. Examples of pharmaceuticals include laninamivir and rifampicin.

count mean std min 25% 50% 75% max
201 4.159825 1.384663 1.762741 3.202318 3.992249 4.690629 8.214511

6_病原生物に対する医薬品.png

Drugs whose main purpose is not treatment

Furthermore, it is classified into dispensing drugs, diagnostic drugs, public health drugs, in-vitro diagnostic drugs, and others. Drugs include adenosine and edrophonium.

count mean std min 25% 50% 75% max
70 3.336593 1.027391 1.054917 2.544872 3.402247 3.976367 5.783386

7_治療を主目的としない医薬品.png

drug

It is further classified into alkaloid narcotics, non-alkaloid narcotics, and others.

count mean std min 25% 50% 75% max
15 3.747792 1.351973 1.977279 2.541722 3.994829 5.00452 5.273602

8_麻薬.png

Is there a significant difference between the classifications?

Welch's t-test was used between each of the two groups.

p-value Nerve / sensory organs Each organ metabolism Tissue cells Pathogenic organisms Non-treatment drug
Nerve / sensory organs - 0.000 0.000 0.000 0.000 0.053 0.076
Each organ 0.000 - 0.225 0.140 0.000 0.453 0.392
metabolism 0.000 0.225 - 0.740 0.000 0.140 0.615
Tissue cells 0.000 0.140 0.740 - 0.000 0.093 0.707
Pathogenic organisms 0.000 0.000 0.000 0.000 - 0.000 0.272
Non-treatment 0.053 0.453 0.140 0.093 0.000 - 0.281
drug 0.076 0.392 0.615 0.707 0.272 0.281 -

It is considered that the average value of neurological and sensory drugs is easier to synthesize than others, and antibiotics, chemotherapeutic drugs, and antiallergic drugs are difficult to synthesize.

Impressions

――It was a good practice for Pandas ――I would like to compare groups even with the target type [^ 3] --Please comment if you point out any mistakes

[^ 3]: KEGG BRITE: Target-based drug classification

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