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 (
    125022, 124984, 124864, 125040, 124545, 
    124306, 124500, 124267, 123527, 123663, 
    122622, 121624, 120857, 120309, 120299, 
    119361, 118451, 118450, 118222, 117510, 
    117207, 117055, 116706, 116944, 116153, 
    115940, 114765, 114227, 113387, 112100
  ) 
  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 0.00121

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 60 Using where

Result

product_id price
112100 1.69000000
113387 1.69000000
114227 1.69000000
114765 1.69000000
115940 1.69000000
116153 1.69000000
116706 1.69000000
116944 1.69000000
117055 1.69000000
117207 1.69000000
117510 1.69000000
118222 1.69000000
118450 1.69000000
118451 1.69000000
119361 1.69000000
120299 1.69000000
120309 1.69000000
120857 1.69000000
121624 1.69000000
122622 1.69000000
123527 1.69000000
123663 1.69000000
124267 1.69000000
124306 1.69000000
124500 1.69000000
124545 1.69000000
124864 1.69000000
124984 1.69000000
125022 1.69000000
125040 1.69000000