Frontiers in Drug Design and Discovery

Volume: 4

Data Modeling and Chemical Interpretation of ADME Properties Using Regression and Rule Mining Techniques

Author(s): Kiyoshi Hasegawa and Kimito Funatsu

Pp: 378-428 (51)

DOI: 10.2174/978160805202810904010378

* (Excluding Mailing and Handling)

Abstract

In pharmaceutical industry, in addition to high potency, good absorption, distribution, metabolism and excretion (ADME) profiles of compounds are needed for drug development. Data modeling of ADME model is a crucial step for efficient drug design. However, we have to avoid so called a situation, the black box, which might be difficult for chemical interpretation. The right balance between precision and interpretation is required for practical drug design.

We review the related articles to focus several ADME modeling techniques. As regression, multiple linear regressions (MLR), partial least squares (PLS), artificial neural networks (ANN), support vector machines (SVM) are picked up and their algorithms and the representative applications are introduced. We pay attention to rule mining methods for chemical interpretation. As rule mining, rough set theory (RST) is shown as an example. Visualization is a classical but never neglected technique for easily understanding the overall behaviors of huge compounds. We especially spend more pages about kohonen neural networks (KNN) and decision trees (DT) as the representative methods. Furthermore, web application for chemists is another important aspect for practical drug design. Recent trend about this topic is shown in two industry cases. As conclusion, we will show future direction concerning in silico ADME prediction.

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      • 16. vendor/laravel/framework/src/Illuminate/Routing/ControllerDispatcher.php:43
      • 17. vendor/laravel/framework/src/Illuminate/Routing/Route.php:260
    • (select j.user_access_id,j.volume_id,j.user_id,j.from_ip,j.to_ip,j.type,j.track,"Trial Access" as access_base_text, CASE j.type WHEN 111 THEN true ELSE false END as terms_popup, "S" as content_download_type, null as restricted_user_access_key, null as restricted_user_access_type, CASE j.track WHEN 0 THEN false ELSE true END as tracksAccessByVolume,"chapter" as access_level, j.chapter_id from `user_access_chapter_trail` as `j` inner join `user_access_info` as `info` on `j`.`user_access_id` = `info`.`user_access_id` where ((j.from_ip <= 873336012 and j.to_ip >=873336012 )) and ((j.from_date <= 1740497167 and j.to_date >= 1740497167 and j.perpetual= 0) or (j.from_date is null and j.to_date is null and j.perpetual= 1)) and j.chapter_id = 2219) union (select j.user_access_id,j.volume_id,j.user_id,j.from_ip,j.to_ip,j.type,j.track,"Subscribed" as access_base_text, false as terms_popup, "S" as content_download_type, null as restricted_user_access_key, null as restricted_user_access_type, CASE j.track WHEN 0 THEN false ELSE true END as tracksAccessByVolume,"chapter" as access_level, j.chapter_id from `user_access_chapter_corporate` as `j` inner join `user_access_info` as `info` on `j`.`user_access_id` = `info`.`user_access_id` where ((j.from_ip <= 873336012 and j.to_ip >=873336012 )) and ((j.from_date <= 1740497167 and j.to_date >= 1740497167 and j.perpetual= 0) or (j.from_date is null and j.to_date is null and j.perpetual= 1)) and j.chapter_id = 2219) union (select j.user_access_id,j.volume_id,j.user_id,j.from_ip,j.to_ip,j.type,j.track,"Token Based Access" as access_base_text, false as terms_popup, "R" as content_download_type, j.uc_id as restricted_user_access_key, "v" as restricted_user_access_type, CASE j.track WHEN 0 THEN false ELSE true END as tracksAccessByVolume,"chapter" as access_level, j.chapter_id from `user_access_chapter_token` as `j` inner join `user_access_info` as `info` on `j`.`user_access_id` = `info`.`user_access_id` where ((j.from_ip <= 873336012 and j.to_ip >=873336012 )) and ((j.from_date <= 1740497167 and j.to_date >= 1740497167 and j.perpetual= 0) or (j.from_date is null and j.to_date is null and j.perpetual= 1)) and j.chapter_id = 2219)
      670μsalphaeurekaselec_live_10_06_2022UserAccess.php#1266
      Backtrace
      • 13. app/Models/UserAccess/UserAccess.php:1266
      • 14. app/Http/Controllers/ChapterController.php:1549
      • 15. vendor/laravel/framework/src/Illuminate/Routing/Controller.php:54
      • 16. vendor/laravel/framework/src/Illuminate/Routing/ControllerDispatcher.php:43
      • 17. vendor/laravel/framework/src/Illuminate/Routing/Route.php:260
    • select b.banner_link, b.banner_name, b.banner_script, b.banner_remarks, b.banner_file_name, b.banner_placement, bd.content_type, bd.content_id from `tbl_banner` as `b` inner join `tbl_banner_detail` as `bd` on `bd`.`banner_id` = `b`.`banner_id` inner join `users` as `u` on `u`.`id` = `b`.`updated_by` where `b`.`banner_ebook` = 1 and `bd`.`content_type` = 'B' and `bd`.`content_id` = 945 and `b`.`banner_from_date` <= 1740497167 and `b`.`banner_to_date` >= 1740497167 and `b`.`banner_status` = 'A' order by `b`.`banner_id` desc
      1.12msalphaeurekaselec_live_10_06_2022Banner.php#95
      Bindings
      • 0: 1
      • 1: B
      • 2: 945
      • 3: 1740497167
      • 4: 1740497167
      • 5: A
      Backtrace
      • 13. app/Models/Banner.php:95
      • 14. app/Http/helpers.php:404
      • 17. vendor/laravel/framework/src/Illuminate/Filesystem/Filesystem.php:124
      • 18. vendor/laravel/framework/src/Illuminate/View/Engines/PhpEngine.php:58
      • 19. vendor/laravel/framework/src/Illuminate/View/Engines/CompilerEngine.php:73
    • select count(*) as aggregate from `uc_cart_products` where cart_id='5a7be31fce7804030af2dfc30bee2464'
      230μsalphaeurekaselec_live_10_06_2022Cart.php#271
      Backtrace
      • 15. app/Models/Cart.php:271
      • 16. view::layouts._header:260
      • 18. vendor/laravel/framework/src/Illuminate/Filesystem/Filesystem.php:124
      • 19. vendor/laravel/framework/src/Illuminate/View/Engines/PhpEngine.php:58
      • 20. vendor/laravel/framework/src/Illuminate/View/Engines/CompilerEngine.php:73
    App\Models\Chapter
    1Chapter.php#?
    App\Models\Ebook
    1Ebook.php#?
        _token
        5syMbqTYUCBMfzNGcbN4EQ5mMRRJsnwhMr8UNda8
        uc_cart_id
        5a7be31fce7804030af2dfc30bee2464
        _previous
        array:1 [ "url" => "https://alpha.eurekaselect.com/chapter/2219" ]
        _flash
        array:2 [ "old" => [] "new" => [] ]
        PHPDEBUGBAR_STACK_DATA
        []
        path_info
        /chapter/2219
        status_code
        200
        
        status_text
        OK
        format
        html
        content_type
        text/html; charset=UTF-8
        request_query
        []
        
        request_request
        []
        
        request_headers
        0 of 0
        array:17 [ "x-https" => array:1 [ 0 => "1" ] "host" => array:1 [ 0 => "alpha.eurekaselect.com" ] "priority" => array:1 [ 0 => "u=0, i" ] "cookie" => array:1 [ 0 => "wayfindertarget=eyJpdiI6IkhhaVBGTnpqRENCVmNtY28zSEdGRFE9PSIsInZhbHVlIjoibHQrcXphcTFjbG5UNjlzaWZEOXpic0QrN09XaVFjejBHLzNqT1lNVThURT0iLCJtYWMiOiI5YmJkZmU4MTkxYjBmNmYwODAyYzk3MDE0OWZkNDYzMTliYTk2YjZhOTVmYzgwYzgxMmMwYzI5ZDhjNTM2YTZhIiwidGFnIjoiIn0%3Dwayfindertarget=eyJpdiI6IkhhaVBGTnpqRENCVmNtY28zSEdGRFE9PSIsInZhbHVlIjoibHQrcXphcTFjbG5UNjlzaWZEOXpic0QrN09XaVFjejBHLzNqT1lNVThURT0iLCJtYWMiOiI5YmJkZmU4MTkxYjBm" ] "accept-encoding" => array:1 [ 0 => "gzip, deflate, br, zstd" ] "sec-fetch-dest" => array:1 [ 0 => "document" ] "sec-fetch-user" => array:1 [ 0 => "?1" ] "sec-fetch-mode" => array:1 [ 0 => "navigate" ] "sec-fetch-site" => array:1 [ 0 => "none" ] "accept" => array:1 [ 0 => "text/html,application/xhtml+xml,application/xml;q=0.9,image/avif,image/webp,image/apng,*/*;q=0.8,application/signed-exchange;v=b3;q=0.7" ] "user-agent" => array:1 [ 0 => "Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com)" ] "upgrade-insecure-requests" => array:1 [ 0 => "1" ] "sec-ch-ua-platform" => array:1 [ 0 => ""Windows"" ] "sec-ch-ua-mobile" => array:1 [ 0 => "?0" ] "sec-ch-ua" => array:1 [ 0 => ""HeadlessChrome";v="129", "Not=A?Brand";v="8", "Chromium";v="129"" ] "cache-control" => array:1 [ 0 => "no-cache" ] "pragma" => array:1 [ 0 => "no-cache" ] ]
        request_cookies
        0 of 0
        array:1 [ "wayfindertarget" => null ]
        response_headers
        0 of 0
        array:5 [ "content-type" => array:1 [ 0 => "text/html; charset=UTF-8" ] "cache-control" => array:1 [ 0 => "no-cache, private" ] "date" => array:1 [ 0 => "Tue, 25 Feb 2025 15:26:07 GMT" ] "set-cookie" => array:2 [ 0 => "XSRF-TOKEN=eyJpdiI6IndHOGQwcUJVTm5JN1RKTjdpRmYzaVE9PSIsInZhbHVlIjoianQwNS9Kd0FSU2cxM3ZtZXhlV2E5bEJyVVg2V3FQVCtPVmY1VWQyTDNNU3ZrVmdodkkvTmVxcG5sWjhjUmMrTUJKSUZWYyt0aG9vTTUrSnJkYUU2ZlVzY2swVVljdlRTMC9TWk13U29MdTN6OVJTS1V2QzFYa2ZmUy8yYng0NU0iLCJtYWMiOiJlZjIyN2IwMTVkMjkyYmJiNTA0YjYxY2E3OWUwMDRhNjIwYjk1ZmRmNjY0Njk0YmQyMWRiN2Y4Y2MyNzk4NjMwIiwidGFnIjoiIn0%3D; expires=Fri, 28 Feb 2025 03:26:07 GMT; Max-Age=216000; path=/; secure; samesite=laxXSRF-TOKEN=eyJpdiI6IndHOGQwcUJVTm5JN1RKTjdpRmYzaVE9PSIsInZhbHVlIjoianQwNS9Kd0FSU2cxM3ZtZXhlV2E5bEJyVVg2V3FQVCtPVmY1VWQyTDNNU3ZrVmdodkkvTmVxcG5sWjhjUmMrTUJKSUZWY" 1 => "alphaeurekaselectnet_session=eyJpdiI6IjRWcThrODJIUUFNNUt3VTFwUnQ5RFE9PSIsInZhbHVlIjoiWWphODZBTU1qYlpuSXhvUmoxSTc4eXdQTDJraWRjZHZQdSt2bXNjL1FGSFJYc093aTd1a0ZqWnZaV2dFeG9OeDJ3dE4ySW16UFVnNWQ2RDlGWDVOaDEvTHRvcWdUUlNicU8raCtwMXdnaXUzNlFZaHladkR0TlVCeU9zL2JURVoiLCJtYWMiOiIzMDViZTdjMmRlYTNiNGVlMzU1ZTBiNjQ2YjE0ZWQ1YmIzMzQzNTM0OTVjZjM1ODBmOWZjOGM2MmZiMjM1ZDlmIiwidGFnIjoiIn0%3D; path=/; secure; httponly; samesite=laxalphaeurekaselectnet_session=eyJpdiI6IjRWcThrODJIUUFNNUt3VTFwUnQ5RFE9PSIsInZhbHVlIjoiWWphODZBTU1qYlpuSXhvUmoxSTc4eXdQTDJraWRjZHZQdSt2bXNjL1FGSFJYc093aTd1a0ZqWnZ" ] "Set-Cookie" => array:2 [ 0 => "XSRF-TOKEN=eyJpdiI6IndHOGQwcUJVTm5JN1RKTjdpRmYzaVE9PSIsInZhbHVlIjoianQwNS9Kd0FSU2cxM3ZtZXhlV2E5bEJyVVg2V3FQVCtPVmY1VWQyTDNNU3ZrVmdodkkvTmVxcG5sWjhjUmMrTUJKSUZWYyt0aG9vTTUrSnJkYUU2ZlVzY2swVVljdlRTMC9TWk13U29MdTN6OVJTS1V2QzFYa2ZmUy8yYng0NU0iLCJtYWMiOiJlZjIyN2IwMTVkMjkyYmJiNTA0YjYxY2E3OWUwMDRhNjIwYjk1ZmRmNjY0Njk0YmQyMWRiN2Y4Y2MyNzk4NjMwIiwidGFnIjoiIn0%3D; expires=Fri, 28-Feb-2025 03:26:07 GMT; path=/; secureXSRF-TOKEN=eyJpdiI6IndHOGQwcUJVTm5JN1RKTjdpRmYzaVE9PSIsInZhbHVlIjoianQwNS9Kd0FSU2cxM3ZtZXhlV2E5bEJyVVg2V3FQVCtPVmY1VWQyTDNNU3ZrVmdodkkvTmVxcG5sWjhjUmMrTUJKSUZWY" 1 => "alphaeurekaselectnet_session=eyJpdiI6IjRWcThrODJIUUFNNUt3VTFwUnQ5RFE9PSIsInZhbHVlIjoiWWphODZBTU1qYlpuSXhvUmoxSTc4eXdQTDJraWRjZHZQdSt2bXNjL1FGSFJYc093aTd1a0ZqWnZaV2dFeG9OeDJ3dE4ySW16UFVnNWQ2RDlGWDVOaDEvTHRvcWdUUlNicU8raCtwMXdnaXUzNlFZaHladkR0TlVCeU9zL2JURVoiLCJtYWMiOiIzMDViZTdjMmRlYTNiNGVlMzU1ZTBiNjQ2YjE0ZWQ1YmIzMzQzNTM0OTVjZjM1ODBmOWZjOGM2MmZiMjM1ZDlmIiwidGFnIjoiIn0%3D; path=/; secure; httponlyalphaeurekaselectnet_session=eyJpdiI6IjRWcThrODJIUUFNNUt3VTFwUnQ5RFE9PSIsInZhbHVlIjoiWWphODZBTU1qYlpuSXhvUmoxSTc4eXdQTDJraWRjZHZQdSt2bXNjL1FGSFJYc093aTd1a0ZqWnZ" ] ]
        session_attributes
        0 of 0
        array:5 [ "_token" => "5syMbqTYUCBMfzNGcbN4EQ5mMRRJsnwhMr8UNda8" "uc_cart_id" => "5a7be31fce7804030af2dfc30bee2464" "_previous" => array:1 [ "url" => "https://alpha.eurekaselect.com/chapter/2219" ] "_flash" => array:2 [ "old" => [] "new" => [] ] "PHPDEBUGBAR_STACK_DATA" => [] ]
        ClearShow all
        Date ↕MethodURLData
        #12025-02-25 15:26:07GET/chapter/2219112192