SELECT 
  cscart_product_prices.product_id, 
  MIN(
    IF(
      cscart_product_prices.percentage_discount = 0, 
      cscart_product_prices.price, 
      cscart_product_prices.price - (
        cscart_product_prices.price * cscart_product_prices.percentage_discount
      )/ 100
    )
  ) AS price 
FROM 
  cscart_product_prices 
WHERE 
  cscart_product_prices.product_id IN (
    88618, 88617, 88616, 88615, 88614, 88613, 
    88612, 88611, 88610, 88609, 88608, 
    88607, 88606, 88605, 88604, 88603, 
    88602, 88601, 88600, 88599, 88598, 
    88597, 88596, 88595, 88650, 88571, 
    88957, 88956, 88955, 88593, 88592, 
    88172, 88169, 88762, 88761, 88543, 
    88542, 88487, 88486, 88449
  ) 
  AND cscart_product_prices.lower_limit = 1 
  AND cscart_product_prices.usergroup_id IN (0, 1) 
GROUP BY 
  cscart_product_prices.product_id

Query time 0.00125

Explain
id select_type table type possible_keys key key_len ref rows Extra
1 SIMPLE cscart_product_prices range usergroup,product_id,lower_limit,usergroup_id usergroup 9 80 Using where

Result

product_id price
88169 1.69000000
88172 1.69000000
88449 1.69000000
88486 1.69000000
88487 1.69000000
88542 1.69000000
88543 1.69000000
88571 1.69000000
88592 1.69000000
88593 1.69000000
88595 1.69000000
88596 1.69000000
88597 1.69000000
88598 1.69000000
88599 1.69000000
88600 1.69000000
88601 1.69000000
88602 1.69000000
88603 1.69000000
88604 1.69000000
88605 1.69000000
88606 1.69000000
88607 1.69000000
88608 1.69000000
88609 1.69000000
88610 1.69000000
88611 1.69000000
88612 1.69000000
88613 1.69000000
88614 1.69000000
88615 1.69000000
88616 1.69000000
88617 1.69000000
88618 1.69000000
88650 1.69000000
88761 1.69000000
88762 1.69000000
88955 1.69000000
88956 1.69000000
88957 1.69000000