<?php

$key = "Main.Sub.SubOfSub";
$target = array('Main' => array('Sub2' => 'Test'));
$value = "SuperData";

$rv = &$target;
foreach(explode('.', $key) as $pk)
{
	$rv = &$rv[$pk];
}
$rv = $value;
unset($rv);

var_dump($target);

array(1) {
  ["Main"]=>
  array(2) {
    ["Sub2"]=>
    string(4) "Test"
    ["Sub"]=>
    array(1) {
      ["SubOfSub"]=>
      string(9) "SuperData"
    }
  }
}