"...I am focus on user1 in the script below but would also like to see a script example if I wanted to in place edit user1 and user3..."

I agree with hdb and others totally here, however, if you still want to practice with your originally Posted data as shown in your post. You can go through the line one by one substituting for user1 and user3 like so:

use warnings;
use strict;

while(<DATA>){
 chomp;
 if(/^user(1|3):/){
    s{(?<=/bin)(.+?)$}{/nologin};
 }
 
  print $_,$/;
}


__DATA__
user1:x:9760822:3241:USER 1:/home/user1:/bin/bash

user2:x:9760822:3242:USER 2:/home/user2:/bin/ksh

user3:x:9760822:3243:USER 3:/home/user3:/bin/sh
[download]

user1:x:9760822:3241:USER 1:/home/user1:/bin/nologin

user2:x:9760822:3242:USER 2:/home/user2:/bin/ksh

user3:x:9760822:3243:USER 3:/home/user3:/bin/nologin
[download]