WASHINGTON - A federal judge dealt Sen. Robert Menendez a setback in his defense against corruption charges Monday, denying most of the New Jersey Democrat's motions to dismiss the case or throw out evidence.

Judge William Walls did toss two bribery counts against Menendez and two facing his friend and political donor, Salomon Melgen. Those charges were related to donations Melgen made to a Menendez legal fund.

But Menendez's most ambitious motions - attempting to have the entire indictment thrown out on grounds of prosecutorial misconduct or violations of constitutional protections - were denied. He still faces 12 counts of bribery, conspiracy, honest-services fraud, and other charges.

Federal prosecutors allege that Melgen, a South Florida eye doctor, showered Menendez with campaign donations and gifts in exchange for the senator's official influence to help in a business dispute, in an $8.9 million Medicare billing fight, and in getting visas for three of the donor's girlfriends. Menendez and Melgen have said they will be exonerated.

Notably, in an era of massive super PAC spending, Walls concluded that Melgen's donations to a Democratic super PAC could form the basis of a bribery charge - despite a controversial Supreme Court ruling that found that donations to outside groups do not risk corruption.

"Notwithstanding the statement in Citizens United that independent expenditures have no actual value to candidates, a jury could find that defendant Menendez placed value, albeit subjective, on the earmarked donations" to a supportive super PAC, the U.S. District Court judge in Newark, N.J., wrote.

Several of Menendez's motions to dismiss the case, or parts of it, were still pending as of Monday evening, and his attorneys pledged to appeal some of Walls' rulings.

"Many of the motions raise important and novel legal questions that often require review by trial and appellate courts," Menendez's lead attorney, Abbe Lowell, said in a statement. "We intend to seek that additional review."

The decisions Monday drew applause from watchdog groups for their take on super PACs, the big-money entities made possible by the Supreme Court's 2010 Citizens United decision.

The April indictment in part cites earmarked donations Melgen made to Majority PAC, which backs Democratic Senate candidates, as Menendez sought reelection in 2012.

Majority PAC then spent heavily on Menendez, as Melgen requested. Menendez lawyers, however, argued that the senator could not benefit from a donation to a third party. Walls disagreed.

"Even if contributions to Majority PAC had no objective value to Menendez, they unquestionably had value to Majority PAC," the judge wrote, adding it is a crime to corruptly seek "anything of value, even for another person or entity, in return for being influenced in the performance of an official act."

That finding is "significant" and "novel" in the world of campaign finance, but also obvious, said Paul S. Ryan, senior counsel at the Washington-based Campaign Legal Center.

"To put it bluntly, Judge Walls stated the obvious, that contributions to super PACs are valuable to office holders and can corrupt them," Ryan said.

He said this case is the first he knows of that alleges corruption based on donations to a super PAC. He hoped that in the long run, similar corruption cases could force the Supreme Court to reconsider its 2010 ruling.

Menendez sought to have the indictment thrown out based on several factors, including prosecutorial misconduct and his contention that the actions he performed were protected by the Constitution's speech and debate clause - which shields legislative acts from prosecution.

Walls dismissed those arguments. "Defendants are correct that attempts to influence a public official through speech alone are protected. But the Constitution does not protect an attempt to influence a public official's acts through improper means, such as the bribery scheme that has been alleged in this case," he wrote.

Walls dismissed the counts related to Melgen's donations to Menendez's legal fund, the Fund to Uphold the Constitution, because those contributions did not meet the standard for a bribery charges. They were made in 2010, while the indictment alleges that Melgen bribed Menendez with donations to help him win reelection in 2012.

Anticipating appeals of his rulings, Walls had previously pushed the trial back to next year, likely in the fall.