Mysql / WordPress killing my server with 80k users

I have recently installed wordpress in a production server with 80K fields in wp_users registered, 175K fields in wp_post table and 350K fields in wp_postmeta. Problem is that mysql database is consuming all CPU and getting server too slow. I disabled all plugings and renamed those plugins folders and problem persists.

top - 20:26:55 up 6 days, 16:01,  1 user,  load average: 4.42, 4.47, 4.54
Tasks: 192 total,   2 running, 190 sleeping,   0 stopped,   0 zombie
%Cpu(s): 55.2 us,  3.4 sy,  0.0 ni, 40.7 id,  0.6 wa,  0.0 hi,  0.2 si,  0.0 st
KiB Mem : 32639948 total,   239032 free,  8069912 used, 24331004 buff/cache
KiB Swap:  8388604 total,  8375548 free,    13056 used. 23506600 avail Mem

  PID USER      PR  NI    VIRT    RES    SHR S  %CPU %MEM     TIME+ COMMAND
 3957 mysql     20   0 1629756 232200   9344 S 384.1  0.7 106:23.68 mysqld

I have monitored mysql with mysql -u admin -p -e SHOW full PROCESSLIST; and gets repeated many times this same query:

| 13489 | mydbnumber1| localhost | mydbnumber1 | Query   |    0 | Copying to tmp table | SELECT wp_users.user_login FROM wp_users INNER JOIN wp_usermeta ON ( wp_users.ID = wp_usermeta.user_id ) WHERE 1=1 AND (
  (
    ( wp_usermeta.meta_key = 'wp_capabilities' AND wp_usermeta.meta_value LIKE '%\administrator\%' )
  )
) ORDER BY user_login ASC |    0.000 |

I have looked for this killer code query into all files of wordpress instalation and only found match in the file named: \wp-admin\includes\deprecated.php line 523. So I decided to comment that pece of code and upload back file deprecated.php to server, but problem persists!

This is crazy now, I have been now 2 days investigating this and I can not find a solution.